Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008592.1 Hibiscus syriacus cultivar Beakdansim tig00111541_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: 876692
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 4 of 4
Found at i:813383 original size:29 final size:29
Alignment explanation
Indices: 813350--813408 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
813340 CGAGCATGCA
813350 ACCATGTCGCCCAG-G-GCACATGGCGACCT
1 ACCATGTCGCCCAGCGTGCACA--GCGACCT
813379 ACCATGTCGCCCAGCGTGCACAGCGACCT
1 ACCATGTCGCCCAGCGTGCACAGCGACCT
813408 A
1 A
813409 ATTATAGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 22 0.79
30 1 0.04
31 5 0.18
ACGTcount: A:0.22, C:0.39, G:0.25, T:0.14
Consensus pattern (29 bp):
ACCATGTCGCCCAGCGTGCACAGCGACCT
Found at i:813517 original size:29 final size:29
Alignment explanation
Indices: 813484--813542 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
813474 TGCAAAGGAT
* *
813484 CAAGGTTGCCCGGAAGGCATGGCGACCTA
1 CAAGGTCGCCCGGAAAGCATGGCGACCTA
813513 CAAGGTCGCCCGGAAAGCATGGCGACCTA
1 CAAGGTCGCCCGGAAAGCATGGCGACCTA
813542 C
1 C
813543 GACCAACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.31, G:0.32, T:0.12
Consensus pattern (29 bp):
CAAGGTCGCCCGGAAAGCATGGCGACCTA
Found at i:821089 original size:18 final size:17
Alignment explanation
Indices: 821066--821119 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
821056 AAAAAGATTC
821066 AATTAAAAATATAAAAAA
1 AATTAAAAATA-AAAAAA
821084 AATTAATAAA-AAATAAAA
1 AATTAA-AAATAAA-AAAA
*
821102 AATGTTAAAATAAAAAAA
1 AAT-TAAAAATAAAAAAA
821120 TATAAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
17 2 0.06
18 21 0.68
19 8 0.26
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (17 bp):
AATTAAAAATAAAAAAA
Found at i:821095 original size:22 final size:23
Alignment explanation
Indices: 821053--821103 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
821043 TTATTGTTAG
* *
821053 ATAAAAAAGATTCAATTAAAAAT
1 ATAAAAAAAATTCAATAAAAAAT
821076 ATAAAAAAAATT-AATAAAAAAT
1 ATAAAAAAAATTCAATAAAAAAT
821098 A-AAAAA
1 ATAAAAA
821104 TGTTAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 5 0.19
22 10 0.38
23 11 0.42
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (23 bp):
ATAAAAAAAATTCAATAAAAAAT
Found at i:822407 original size:2 final size:2
Alignment explanation
Indices: 822402--822798 Score: 225
Period size: 2 Copynumber: 205.5 Consensus size: 2
822392 AATAATAATA
* *
822402 AT AT AT A- AT AT CAT AT A- AT AA AT AT AT AGT A- AT AA AT A- AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
822442 ACT AT AA AT AGT AT AT A- AT AT AT AT ACT AT AC AA AT AT AT AT
1 A-T AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* *
822484 ACT AT ACT AT A- AT AT AT AT AT AC ACT A- AT AT AT AC AT AT A-
1 A-T AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * *
822524 AT AT AT A- AT AT ACC AT AT AA AT AT AT ACT AT AA AT A- AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
822566 AT AT AT AT AT AT AT AT AT AT AT AT ACT A- AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
*
822607 AC AT AT A- AT AT AT A- AT AT A- AT ACT AT ACT AT AT A- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT
*
822646 AT AT -T AT AT A- AT AT GA- AT CAT AT AA AT AT AT AT -T AT AT A-
1 AT AT AT AT AT AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT
* *
822685 AT A- AT AT A- AC AT A- AT AT AT A- AT ACT AT AT AT -T AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
822723 AT AT -T AT AT -T AT AT AT ACT AT AT A- AT AT CAT AT -T AT AT A-
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT -AT AT AT AT AT AT
*
822762 AA AT A- AT AT AT ACT AT AGT AT A- AT ACT AT AT -T AT AT A
1 AT AT AT AT AT AT A-T AT A-T AT AT AT A-T AT AT AT AT AT A
822799 AAAAAATCGA
Statistics
Matches: 313, Mismatches: 26, Indels: 112
0.69 0.06 0.25
Matches are distributed among these distances:
1 35 0.11
2 239 0.76
3 39 0.12
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:822417 original size:5 final size:5
Alignment explanation
Indices: 822404--822799 Score: 135
Period size: 5 Copynumber: 78.2 Consensus size: 5
822394 TAATAATAAT
* *
822404 ATATA ATATC ATATA ATA-A ATAT- ATAGTA ATA-A ATAATA CTATA A-ATA
1 ATATA ATATA ATATA ATATA ATATA ATA-TA ATATA AT-ATA ATATA ATATA
* * * *
822452 GTATATA ATAT- ATATA CTATA CAAATA TATATA CTATA CTATA ATATA
1 --ATATA ATATA ATATA ATATA -ATATA -ATATA ATATA ATATA ATATA
822500 TATATA CACTA-A TATATA CATATAA TATATA ATATA CCATATA A-AT-
1 -ATATA -A-TATA -ATATA -ATAT-A -ATATA ATATA --ATATA ATATA
*
822546 ATATA CTATA A-ATA ATAT- ATATA TATATA TATATA TATATA TATACTA
1 ATATA ATATA ATATA ATATA ATATA -ATATA -ATATA -ATATA -ATA-TA
*
822594 ATAT- ATAT- ATATA ACAT- ATA-A TATATA ATATA ATACT- ATACT-
1 ATATA ATATA ATATA ATATA ATATA -ATATA ATATA ATA-TA ATA-TA
* *
822636 ATATA AT-TA TATATT ATATA ATATGA ATCAT- ATA-A ATAT- ATATT
1 ATATA ATATA -ATATA ATATA ATAT-A AT-ATA ATATA ATATA ATATA
* * *
822680 ATAT- A-ATA ATATA ACATA ATAT- ATAATA CTAT- ATATT ATATA A-ATA
1 ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA ATATA ATATA
* * * * *
822726 TTATA TTAT- ATATA CTATATA ATATC ATATT ATATA AAATA ATATA TACTATA
1 ATATA ATATA ATATA --ATATA ATATA ATATA ATATA ATATA ATATA -A-TATA
* *
822779 GTATA ATACT- ATATT ATATA A
1 ATATA ATA-TA ATATA ATATA A
822800 AAAAATCGAA
Statistics
Matches: 307, Mismatches: 36, Indels: 96
0.70 0.08 0.22
Matches are distributed among these distances:
3 3 0.01
4 64 0.21
5 152 0.50
6 60 0.20
7 28 0.09
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:822704 original size:79 final size:77
Alignment explanation
Indices: 822396--822799 Score: 305
Period size: 83 Copynumber: 5.1 Consensus size: 77
822386 TAAAAAAATA
* * * * *
822396 ATAATA-ATATATAATATCATATAATAAATAT-ATAGTA-ATAAATAATACTATAA-ATAGTATA
1 ATAATATATATATTATATAATATAATATATATAATA-TATATATATAATAATATAACATA-TATA
*
822457 TAATATATATACTAT
64 TAATA-CTATACTAT
* * * *
822472 ACAAATATATATACTATACTATAATATATATATACACTAATATATACATATAAT-ATATAATATA
1 A-TAATATATATA-T-TA-TATAATATA-ATATATA-TAATATATATATATAATAATATAACATA
*
822536 CCATATAAATA-TATACTAT
60 -TATAT-AATACTATACTAT
* *
822555 AAATAATATATATATATATATATATATATATATATACTAATATATATATATAA-CATATAATATA
1 --ATAATATATATAT-TATATA-ATATA-ATATATA-TAATATATATATATAATAATATAACATA
822619 TAATATAATACTATACTAT
60 T-ATATAATACTATACTAT
822638 ATAAT-TATATATTATATAATATGAATCATATA-AATATATATTATATAATAATATAACATAATA
1 ATAATATATATATTATATAATAT-AAT-ATATATAATATATA-TATATAATAATATAACAT-ATA
822701 TATAATACTATA-TAT
62 TATAATACTATACTAT
* *
822716 -T-ATATAAATATTATATTATAT-ATACTATATAATATCATATTATATAAAATAATATATAC-TA
1 ATAATATATATATTATATAATATAATA-TATATAATAT-ATA-TATAT--AATAATATA-ACATA
*
822777 TAGTATAATACTATATTAT
60 TA-TATAATACTATACTAT
822796 ATAA
1 ATAA
822800 AAAAATCGAA
Statistics
Matches: 277, Mismatches: 18, Indels: 60
0.78 0.05 0.17
Matches are distributed among these distances:
74 1 0.00
75 6 0.02
76 8 0.03
77 37 0.13
78 24 0.09
79 56 0.20
80 15 0.05
81 14 0.05
82 14 0.05
83 70 0.25
84 27 0.10
85 5 0.02
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (77 bp):
ATAATATATATATTATATAATATAATATATATAATATATATATATAATAATATAACATATATATA
ATACTATACTAT
Found at i:823766 original size:20 final size:20
Alignment explanation
Indices: 823736--823785 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
823726 TTGAGAGGTT
*
823736 TCGAGTTAACTC-GAACCGAA
1 TCGAGTCAACTCAG-ACCGAA
*
823756 TTGAGTCAACTCAGACCGAA
1 TCGAGTCAACTCAGACCGAA
823776 TCGAGTCAAC
1 TCGAGTCAAC
823786 CCAAATTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGAGTCAACTCAGACCGAA
Found at i:827105 original size:105 final size:104
Alignment explanation
Indices: 826917--827139 Score: 252
Period size: 105 Copynumber: 2.1 Consensus size: 104
826907 GAGTCGAGGG
* *
826917 TCTACGCGGTCCTTCGGGACATATAGGTATCATATGGAACATCTATGAGGTACTTTGCGACACAT
1 TCTACGTGGTCCTTCGGGACATATAGGTATCATATGGAACATCTATGAGGTACTTTGAGACACAT
* * *
826982 ATTTGGTCCTTAGCATATGTATATGATTCTTAAGGAATTT
66 ACTTGATCCTTAGCATATGTATATGATTCTAAAGGAA-TT
* * * * *
827022 TCTACGTGGTCCTTCGGGACGTATATGTATTC-TTTGGAGCATGTATGAGGT-CTTTTGAGACAC
1 TCTACGTGGTCCTTCGGGACATATAGGTA-TCATATGGAACATCTATGAGGTAC-TTTGAGACAC
* * * * *
827085 TTACTTGATCTTTGGTATATGTATATGGTTCTAAAGGAATT
64 ATACTTGATCCTTAGCATATGTATATGATTCTAAAGGAATT
* *
827126 TATATGTGGTCCTT
1 TCTACGTGGTCCTT
827140 ATGGACAATC
Statistics
Matches: 99, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
104 15 0.15
105 82 0.83
106 2 0.02
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (104 bp):
TCTACGTGGTCCTTCGGGACATATAGGTATCATATGGAACATCTATGAGGTACTTTGAGACACAT
ACTTGATCCTTAGCATATGTATATGATTCTAAAGGAATT
Found at i:828158 original size:21 final size:21
Alignment explanation
Indices: 828132--828174 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
828122 TTTCTGGATT
* *
828132 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
828153 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
828174 A
1 A
828175 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:828249 original size:67 final size:68
Alignment explanation
Indices: 828154--828305 Score: 216
Period size: 68 Copynumber: 2.2 Consensus size: 68
828144 ACCCATTCAA
* * *
828154 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
828218 GGG
66 GGG
* * * *
828221 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
828286 GGG
66 GGG
* *
828289 GAGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
828306 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 26 0.35
68 49 0.65
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:828670 original size:28 final size:29
Alignment explanation
Indices: 828607--828677 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 29
828597 CATATTATGA
**
828607 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
828636 TACATGACATGAATTCATA-TATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
828664 TACATGACATGAAT
1 TACATGACATGAAT
828678 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 22 0.56
29 17 0.44
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:828734 original size:30 final size:31
Alignment explanation
Indices: 828692--828751 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
828682 AGAAAAAGTT
*
828692 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
828723 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
828752 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:829045 original size:22 final size:22
Alignment explanation
Indices: 828971--829037 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
828961 TTATGGACAT
828971 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
828993 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
829015 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
829037 A
1 A
829038 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:835094 original size:21 final size:21
Alignment explanation
Indices: 835068--835110 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
835058 TTTCTGGATT
* *
835068 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
835089 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
835110 A
1 A
835111 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:835185 original size:67 final size:68
Alignment explanation
Indices: 835090--835241 Score: 216
Period size: 68 Copynumber: 2.2 Consensus size: 68
835080 ACCCATTCAA
* * *
835090 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
835154 GGG
66 GGG
* * * *
835157 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
835222 GGG
66 GGG
* *
835225 GAGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
835242 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 26 0.35
68 49 0.65
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:835578 original size:29 final size:29
Alignment explanation
Indices: 835544--835615 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
835534 CATATTATGA
**
835544 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
835573 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
835602 TACATGACATGAAT
1 TACATGACATGAAT
835616 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:835672 original size:30 final size:31
Alignment explanation
Indices: 835630--835689 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
835620 AGAAAAAGTT
*
835630 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
835661 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
835690 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:835983 original size:22 final size:22
Alignment explanation
Indices: 835909--835975 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
835899 TTATGGACAT
835909 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
835931 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
835953 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
835975 A
1 A
835976 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:854789 original size:28 final size:28
Alignment explanation
Indices: 854745--854808 Score: 119
Period size: 28 Copynumber: 2.2 Consensus size: 28
854735 ACATCTTCTT
854745 ATAGTTGGGGGATCATTTTATAACTTTTA
1 ATAGTT-GGGGATCATTTTATAACTTTTA
854774 ATAGTTGGGGATCATTTTATAACTTTTA
1 ATAGTTGGGGATCATTTTATAACTTTTA
854802 ATAGTTG
1 ATAGTTG
854809 AAAGACCCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 29 0.83
29 6 0.17
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.45
Consensus pattern (28 bp):
ATAGTTGGGGATCATTTTATAACTTTTA
Found at i:855497 original size:14 final size:14
Alignment explanation
Indices: 855475--855521 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
855465 CCTCGCATAG
* *
855475 CTCGCTCGGATGGC
1 CTCGGTCGGATGAC
*
855489 CTCGGTCGGATGCC
1 CTCGGTCGGATGAC
855503 CTCGGTCGGATGAC
1 CTCGGTCGGATGAC
855517 CTCGG
1 CTCGG
855522 ATGCTCTCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.09, C:0.34, G:0.36, T:0.21
Consensus pattern (14 bp):
CTCGGTCGGATGAC
Found at i:857175 original size:27 final size:27
Alignment explanation
Indices: 857129--857186 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
857119 ATTTCATAGA
857129 AATAATATTATTAAATTA-TTAATAATT
1 AATAATATTATTAAATTATTTAAT-ATT
*
857156 AATAATATTATT-TATATATTTAATATT
1 AATAATATTATTAAAT-TATTTAATATT
857183 AATA
1 AATA
857187 TAATAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
27 21 0.75
28 5 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
AATAATATTATTAAATTATTTAATATT
Found at i:857232 original size:23 final size:23
Alignment explanation
Indices: 857206--857250 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
857196 AATAATATTT
857206 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
857229 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
857251 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:857369 original size:13 final size:13
Alignment explanation
Indices: 857331--857369 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
857321 TATTAATATT
*
857331 TTTATTAATAAAA
1 TTTAATAATAAAA
*
857344 TTATAAAAATAAAA
1 TT-TAATAATAAAA
857358 TTTAATAATAAA
1 TTTAATAATAAA
857370 TAAATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTAATAATAAAA
Found at i:857419 original size:25 final size:24
Alignment explanation
Indices: 857355--857422 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 24
857345 TATAAAAATA
* *
857355 AAATTTAATAATAAATAAATTATTTT
1 AAATTTTAT-ATAAAT-AATTATATT
857381 AATATTTTA-A-AAATAATTATATT
1 AA-ATTTTATATAAATAATTATATT
857404 AAATTTTATGATAAATAAT
1 AAATTTTAT-ATAAATAAT
857423 ATTATTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 5 0.14
25 8 0.22
26 2 0.06
27 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (24 bp):
AAATTTTATATAAATAATTATATT
Found at i:858987 original size:26 final size:26
Alignment explanation
Indices: 858958--859009 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
858948 ACATTGATTT
858958 GTTTTAATGTGATCATTGGAATTTTG
1 GTTTTAATGTGATCATTGGAATTTTG
858984 GTTTTAATGTGATCATTGGAATTTTG
1 GTTTTAATGTGATCATTGGAATTTTG
859010 ATATACATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.04, G:0.23, T:0.50
Consensus pattern (26 bp):
GTTTTAATGTGATCATTGGAATTTTG
Found at i:863246 original size:29 final size:30
Alignment explanation
Indices: 863193--863251 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
863183 TATGCAGAAA
*
863193 TTGATGTTCTTTTTATATACACTTTATGAG
1 TTGATGTTATTTTTATATACACTTTATGAG
863223 TTGATGTTATTTTTATATA-ACTTTATGAG
1 TTGATGTTATTTTTATATACACTTTATGAG
863252 CTATTCAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (30 bp):
TTGATGTTATTTTTATATACACTTTATGAG
Found at i:871031 original size:16 final size:16
Alignment explanation
Indices: 871010--871049 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
871000 GATTAATTGT
*
871010 TTTCAGTTCGGGTTAC
1 TTTCAGTTCAGGTTAC
871026 TTTCAGTTCAGGTTAC
1 TTTCAGTTCAGGTTAC
871042 TTTCAGTT
1 TTTCAGTT
871050 TGGTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.47
Consensus pattern (16 bp):
TTTCAGTTCAGGTTAC
Found at i:871086 original size:26 final size:26
Alignment explanation
Indices: 871032--871082 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
871022 TTACTTTCAG
*
871032 TTCAGGTTACTTTCAGTTTGGTTAAA
1 TTCAGGTCACTTTCAGTTTGGTTAAA
*
871058 TTCAGGTCA-TTTCGGTTTGGTTAAA
1 TTCAGGTCACTTTCAGTTTGGTTAAA
871083 ATTCGGGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.45
Consensus pattern (26 bp):
TTCAGGTCACTTTCAGTTTGGTTAAA
Found at i:875199 original size:79 final size:78
Alignment explanation
Indices: 875113--875270 Score: 255
Period size: 79 Copynumber: 2.0 Consensus size: 78
875103 CTCAATAACA
875113 TATAAAAATATGTT-TACATACAATATAAATTTTAAAATTATTAAATAGATTAAATAATTTAATT
1 TATAAAAATAT-TTGTACATACAATATAAATTTTAAAATTATTAAATAGATT-AATAATTTAATT
*
875177 TAATGATTATATTTG
64 TAATGATTATACTTG
* * *
875192 TATAAAAATATTTGTATATACAATATAAATTTTAAATTTATTAAATATATTAATAATTTAATTTA
1 TATAAAAATATTTGTACATACAATATAAATTTTAAAATTATTAAATAGATTAATAATTTAATTTA
875257 ATGATTATACTTG
66 ATGATTATACTTG
875270 T
1 T
875271 TTTGAATTTG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
78 29 0.39
79 45 0.61
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (78 bp):
TATAAAAATATTTGTACATACAATATAAATTTTAAAATTATTAAATAGATTAATAATTTAATTTA
ATGATTATACTTG
Found at i:875759 original size:14 final size:14
Alignment explanation
Indices: 875742--875773 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
875732 TCCTTTCTCT
875742 TCTTCCTCTTCAAA
1 TCTTCCTCTTCAAA
875756 TCTTCCTCTTCAAA
1 TCTTCCTCTTCAAA
875770 TCTT
1 TCTT
875774 TATCTTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.19, C:0.34, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTTCCTCTTCAAA
Found at i:875779 original size:14 final size:14
Alignment explanation
Indices: 875742--875781 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
875732 TCCTTTCTCT
*
875742 TCTTCCTCTTCAAA
1 TCTTCATCTTCAAA
*
875756 TCTTCCTCTTCAAA
1 TCTTCATCTTCAAA
*
875770 TCTTTATCTTCA
1 TCTTCATCTTCA
875782 TAGCTCTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTTCATCTTCAAA
Found at i:876322 original size:21 final size:20
Alignment explanation
Indices: 876296--876339 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
876286 GTATCAATAC
876296 TTGTAGAAAGTATCGAAACTT
1 TTGTAGAAA-TATCGAAACTT
* * *
876317 TTGTAGGAATATCTATACTT
1 TTGTAGAAATATCGAAACTT
876337 TTG
1 TTG
876340 GGTTAGTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (20 bp):
TTGTAGAAATATCGAAACTT
Done.