Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004839.1 Hibiscus syriacus cultivar Beakdansim tig00010907_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: 64207
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:4485 original size:36 final size:36
Alignment explanation
Indices: 4438--4510 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
4428 TCTTGGTTTG
*
4438 CTGCTAGTTTTGACGCTGTGCGGATCCCTTTCGACT
1 CTGCTAGTTTTGACGCTGTGCAGATCCCTTTCGACT
4474 CTGCTAGTTTTGACGCTGTGCAGATCCCTTTCGACT
1 CTGCTAGTTTTGACGCTGTGCAGATCCCTTTCGACT
4510 C
1 C
4511 CCTAGTGGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.12, C:0.29, G:0.23, T:0.36
Consensus pattern (36 bp):
CTGCTAGTTTTGACGCTGTGCAGATCCCTTTCGACT
Found at i:16814 original size:21 final size:21
Alignment explanation
Indices: 16790--16842 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
16780 GAGTTTATTT
*
16790 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTTCATATTTT-AAAAA
16811 TCATTTTT-ATATTTTAAAAA
1 TCATTTTTCATATTTTAAAAA
*
16831 TAATTTTTCATA
1 TCATTTTTCATA
16843 ATCCGAAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (21 bp):
TCATTTTTCATATTTTAAAAA
Found at i:21550 original size:17 final size:16
Alignment explanation
Indices: 21520--21555 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
21510 CAAAAAATTA
21520 AATATATAAATTTTTTG
1 AATATAT-AATTTTTTG
*
21537 AATATCTAATTTTTTG
1 AATATATAATTTTTTG
21553 AAT
1 AAT
21556 TGAATATCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
AATATATAATTTTTTG
Found at i:23414 original size:2 final size:2
Alignment explanation
Indices: 23407--23436 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23397 TTTATTTTGA
23407 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
23437 TATTTAGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32756 original size:216 final size:215
Alignment explanation
Indices: 32483--33040 Score: 860
Period size: 216 Copynumber: 2.6 Consensus size: 215
32473 ACTTTATGAA
* * * *
32483 AAATACAAATTTA-AGAATTAAATTGAACAAATATGAAATTGCAAATAAAAGTTTAAATAAATTA
1 AAATA-AAATTTAGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTA
32547 AACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACA
65 AACAACACA-ATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACA
*
32612 AAAAAATACTAAATTATACCCATTTAAAAAGTTATGGGCCAAATAAAAAATAGAATTAAGTAAAA
129 AAAAAATACTAAATTATACCCATTTAAAAAGTTATGGGCCAAATAAAAAATAGAAATAAGTAAAA
32677 AGTAT-GGATCAATTTCATATGC
194 AGTATAGG-TCAATTTCATATGC
*
32699 AAATAAAATTTAGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATTAATTAA
1 AAATAAAATTTAGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
32764 ACAACACATATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAA
66 ACAACACA-ATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAA
* * * *
32829 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAA
130 AAAAATACTAAATTATACCCATTTAAAAAGTTATGGGCCAAATAAAAAATAGAAATAAGTAAAAA
*
32894 GTATAGGTTAATTTCATATGC
195 GTATAGGTCAATTTCATATGC
* * * *
32915 AAATAAAATTTGGAGGACTAAATTGAATAAATATAAAATTACAAATAAAAATTTAAATAAACTAA
1 AAATAAAATTTAGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
** * *
32980 ACAACACAA---A--AGGGATCCGATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAA
66 ACAACACAATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAA
33040 A
131 A
33041 GTGTACTTGT
Statistics
Matches: 319, Mismatches: 21, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
210 47 0.15
212 1 0.00
215 8 0.03
216 261 0.82
217 2 0.01
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (215 bp):
AAATAAAATTTAGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
ACAACACAATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAA
AAAATACTAAATTATACCCATTTAAAAAGTTATGGGCCAAATAAAAAATAGAAATAAGTAAAAAG
TATAGGTCAATTTCATATGC
Found at i:33384 original size:19 final size:19
Alignment explanation
Indices: 33360--33398 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
33350 TCGAATGCAT
33360 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
33379 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
33398 T
1 T
33399 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:33523 original size:64 final size:65
Alignment explanation
Indices: 33346--33508 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 65
33336 GAATTAATTG
* * * *
33346 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** ** **
33411 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
33475 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
33509 TGGTGCACCG
Statistics
Matches: 84, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
64 40 0.48
65 44 0.52
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:39331 original size:20 final size:21
Alignment explanation
Indices: 39302--39357 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
39292 TTTGTGCTTC
*
39302 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
39322 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
39344 ATGCATCGATGCAT
1 ATGCATCGATGCAT
39358 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:40928 original size:21 final size:21
Alignment explanation
Indices: 40886--40929 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
40876 ACCCCGGGAG
*
40886 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
40907 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
40928 CT
1 CT
40930 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:41991 original size:19 final size:19
Alignment explanation
Indices: 41967--42005 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
41957 TCGAATGCAT
41967 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
41986 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
42005 T
1 T
42006 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:42022 original size:65 final size:64
Alignment explanation
Indices: 41904--42067 Score: 174
Period size: 65 Copynumber: 2.5 Consensus size: 64
41894 TATTCAAAGG
*
41904 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAATTAATTGAACATCGAATGCAT
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC-ATGAATTAATTAAACATCGAATGCAT
41967 TC
63 TC
*
41969 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGAA-TATTTTCAAAACATCGAATGCAT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATTA-ATT--AAACATCGAATGCAT
*
42032 TT
63 TC
* * ***
42034 GATGCATCGATGCACAAGCCATGCATCGATGCAC
1 CATGCACCGATGCACTCTCCATGCATCGATGCAC
42068 ACTTGGTGCA
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
62 2 0.02
63 6 0.07
64 16 0.19
65 60 0.70
66 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATTAATTAAACATCGAATGCATTC
Found at i:43034 original size:2 final size:2
Alignment explanation
Indices: 43029--43127 Score: 58
Period size: 2 Copynumber: 47.5 Consensus size: 2
43019 AAAACAACTA
* * * *
43029 AT AT AT AT AT AT AA ACT AT AT AGT TT AT AT AT AA AGT AT AT GT
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT A-T AT AT AT
* * *
43072 AT -T AT AT AT AT AA ACT AT AT AGT TT AT AT AT AT AT AT -T AT GT
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT
*
43114 AT AA ACT AT AT AT A
1 AT AT A-T AT AT AT A
43128 CCATGTATAA
Statistics
Matches: 73, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
1 2 0.03
2 65 0.89
3 6 0.08
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:43057 original size:22 final size:22
Alignment explanation
Indices: 43032--43105 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
43022 ACAACTAATA
43032 TATATATATAAACTATATAG-T
1 TATATATATAAACTATATAGTT
*
43053 T-TATATATAAAGTATAT-GTAT
1 TATATATATAAACTATATAGT-T
43074 TATATATATAAACTATATAGTT
1 TATATATATAAACTATATAGTT
43096 TATATATATA
1 TATATATATA
43106 TATTATGTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.02
20 15 0.32
21 3 0.06
22 26 0.55
23 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (22 bp):
TATATATATAAACTATATAGTT
Found at i:43124 original size:42 final size:42
Alignment explanation
Indices: 43035--43125 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
43025 ACTAATATAT
*
43035 ATATATAAACTATATAGTTTATATATAAAGTATATGTATTAT
1 ATATATAAACTATATAGTTTATATATAAAGTATATGTATTAA
*
43077 ATATATAAACTATATAGTTTATATATATA-TATTATGTA-TAA
1 ATATATAAACTATATAGTTTATATATAAAGTA-TATGTATTAA
43118 ACTATATA
1 A-TATATA
43126 TACCATGTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 5 0.11
42 40 0.89
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (42 bp):
ATATATAAACTATATAGTTTATATATAAAGTATATGTATTAA
Found at i:43209 original size:11 final size:11
Alignment explanation
Indices: 43195--43232 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
43185 CCTACATAGT
43195 TTATATATAAA
1 TTATATATAAA
*
43206 TTATATATGAA
1 TTATATATAAA
43217 TTATATATAAA
1 TTATATATAAA
*
43228 CTATA
1 TTATA
43233 CAATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:43258 original size:17 final size:17
Alignment explanation
Indices: 43238--43291 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
43228 CTATACAATT
* *
43238 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
43255 TATAATTATAAATAATA
1 TATATTTATAAATTATA
43272 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
43290 TA
1 TA
43292 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:43304 original size:142 final size:140
Alignment explanation
Indices: 43024--43297 Score: 340
Period size: 142 Copynumber: 2.0 Consensus size: 140
43014 AAATTAAAAC
* * * * *
43024 AACTAATATATATATATAAACTATATAGTTTATATATAAAGTATATGTATTATATATATAAACTA
1 AACTAATAAATATATAGAAACTACATAGTTTATATATAAAGTATATATAATATATATATAAACTA
* * * *
43089 TATAGTTTATATATATATATTATGTATAAACTATATATACCATGTATAAACTATAATACTATATA
66 TACAATTTATATATATATATTATGTATAAACTATAAATA-CATATATAAACTATAATACTATATA
43154 GTTTATATATG
130 GTTTATATATG
* *
43165 AACTAATAAACTATATAGAACCTACATAGTTTATATATAAATTATATATGAAT-TATATATAAAC
1 AACTAATAAA-TATATAGAAACTACATAGTTTATATATAAAGTATATAT-AATATATATATAAAC
* * *** *
43229 TATACAATTTATATTTATATATTATGTAT-AATTATAAATA-ATATATATTGTATAA-ATTATAT
64 TATACAATTTATATATATATATTATGTATAAACTATAAATACATATATAAACTATAATACTATAT
43291 AGTTTAT
129 AGTTTAT
43298 TAATATAAAC
Statistics
Matches: 114, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
138 13 0.11
139 11 0.10
141 18 0.16
142 70 0.61
143 2 0.02
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (140 bp):
AACTAATAAATATATAGAAACTACATAGTTTATATATAAAGTATATATAATATATATATAAACTA
TACAATTTATATATATATATTATGTATAAACTATAAATACATATATAAACTATAATACTATATAG
TTTATATATG
Found at i:43485 original size:35 final size:35
Alignment explanation
Indices: 43408--43488 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
43398 ATTTAGGGTT
43408 TATATTTATATTTATATTCATATAAACTACATACTA
1 TATATTTATATTTATATT-ATATAAACTACATACTA
* * *
43444 TA-ATTTATATTTATATT-TATATACTATATTCTA
1 TATATTTATATTTATATTATATAAACTACATACTA
43477 TACTATTTATAT
1 TA-TATTTATAT
43489 AAACTATAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
33 15 0.38
35 23 0.57
36 2 0.05
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (35 bp):
TATATTTATATTTATATTATATAAACTACATACTA
Found at i:43521 original size:33 final size:32
Alignment explanation
Indices: 43475--43573 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 32
43465 TACTATATTC
*
43475 TATACTATTTATATAAACTATAGTTTATATTTA
1 TATACTATATATAT-AACTATAGTTTATATTTA
*
43508 TATACTATATATATGAACTATAGTTTACA--TA
1 TATACTATATATAT-AACTATAGTTTATATTTA
* *
43539 TGA-ACTATATATATAA-TAAAGTTGATATTTA
1 T-ATACTATATATATAACTATAGTTTATATTTA
43570 TATA
1 TATA
43574 TGAACTATAG
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
29 8 0.14
30 3 0.05
31 18 0.32
32 1 0.02
33 26 0.46
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (32 bp):
TATACTATATATATAACTATAGTTTATATTTA
Found at i:43539 original size:18 final size:18
Alignment explanation
Indices: 43518--43680 Score: 118
Period size: 18 Copynumber: 8.7 Consensus size: 18
43508 TATACTATAT
43518 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
43536 ATATGAACTATA-TATAT
1 ATATGAACTATAGTTTAC
* * *
43553 A-ATAAAGTTGATA-TTTAT
1 ATATGAA-CT-ATAGTTTAC
43571 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
43589 ATATAAACTATATAGTTTAT
1 ATATGAAC--TATAGTTTAC
43609 ATACT-AACTATAGTTTAC
1 ATA-TGAACTATAGTTTAC
*
43627 ATATAAACTATAGTTGATATTTAC
1 ATATGAACTATA---G---TTTAC
*
43651 ATATGAACCATAGTTTAC
1 ATATGAACTATAGTTTAC
43669 ATATGAACTATA
1 ATATGAACTATA
43681 TATATAAACT
Statistics
Matches: 117, Mismatches: 14, Indels: 28
0.74 0.09 0.18
Matches are distributed among these distances:
16 4 0.03
17 9 0.08
18 67 0.57
19 4 0.03
20 15 0.13
21 3 0.03
24 15 0.13
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (18 bp):
ATATGAACTATAGTTTAC
Found at i:43645 original size:80 final size:75
Alignment explanation
Indices: 43558--43705 Score: 215
Period size: 80 Copynumber: 1.9 Consensus size: 75
43548 TATATAATAA
* * *
43558 AGTTGATATTTATATATGAACTATAGTTTACATATAAACTATATAGTTTATATACTAACTATAGT
1 AGTTGATATTTACATATGAACCATAGTTTACATATAAACTATATA---TATAAACT-A-TATAGT
43623 TTACATATAAACTAT
61 TTACATATAAACTAT
*
43638 AGTTGATATTTACATATGAACCATAGTTTACATATGAACTATATATATAAACTATATAGTTTACA
1 AGTTGATATTTACATATGAACCATAGTTTACATATAAACTATATATATAAACTATATAGTTTACA
43703 TAT
66 TAT
43706 GACCTATATA
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
75 14 0.22
76 1 0.02
77 7 0.11
80 42 0.66
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.41
Consensus pattern (75 bp):
AGTTGATATTTACATATGAACCATAGTTTACATATAAACTATATATATAAACTATATAGTTTACA
TATAAACTAT
Found at i:43697 original size:33 final size:33
Alignment explanation
Indices: 43660--43726 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
43650 CATATGAACC
43660 ATAGTTTACATATGAACTATATATATAAACTAT
1 ATAGTTTACATATGAACTATATATATAAACTAT
* *
43693 ATAGTTTACATATGACCTATATATATATACTAT
1 ATAGTTTACATATGAACTATATATATAAACTAT
43726 A
1 A
43727 GTTGATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.40
Consensus pattern (33 bp):
ATAGTTTACATATGAACTATATATATAAACTAT
Found at i:43798 original size:51 final size:52
Alignment explanation
Indices: 43688--43799 Score: 154
Period size: 51 Copynumber: 2.2 Consensus size: 52
43678 ATATATATAA
* * *
43688 ACTATATAGTTTACATATGACCTATATATATATACTATAGTTGATATTTATAT
1 ACTATATAGTTTACAGATGACC-ATATATATATACTATAATTGATATTTACAT
* * *
43741 ATTATATAGTTTACAGATGACC-TATATATATACTATAATTTATGTTTACAT
1 ACTATATAGTTTACAGATGACCATATATATATACTATAATTGATATTTACAT
43792 ACTATATA
1 ACTATATA
43800 TTATATATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
51 32 0.62
53 20 0.38
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (52 bp):
ACTATATAGTTTACAGATGACCATATATATATACTATAATTGATATTTACAT
Found at i:43817 original size:51 final size:51
Alignment explanation
Indices: 43688--43821 Score: 126
Period size: 51 Copynumber: 2.6 Consensus size: 51
43678 ATATATATAA
* * * * *
43688 ACTATATAGTTTACATATGACCTATATATATATACTATAGTTGATATTTATAT
1 ACTATATAGTTTACAGATAAAC--TATATATATACTATAATTGATATTTACAT
* * * * *
43741 ATTATATAGTTTACAGATGACCTATATATATACTATAATTTATGTTTACAT
1 ACTATATAGTTTACAGATAAACTATATATATACTATAATTGATATTTACAT
* *
43792 ACTATATA-TTATATATATAAACTATATATA
1 ACTATATAGTT-TACAGATAAACTATATATA
43822 CTATATAGTA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
50 2 0.03
51 47 0.68
53 20 0.29
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (51 bp):
ACTATATAGTTTACAGATAAACTATATATATACTATAATTGATATTTACAT
Found at i:43935 original size:9 final size:9
Alignment explanation
Indices: 43923--43955 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
43913 TACTATAGTA
43923 TATATAAAC
1 TATATAAAC
43932 TATATAATA-
1 TATATAA-AC
43941 TATATAAAC
1 TATATAAAC
43950 TATATA
1 TATATA
43956 TTATATAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (9 bp):
TATATAAAC
Found at i:43942 original size:18 final size:18
Alignment explanation
Indices: 43916--44116 Score: 164
Period size: 18 Copynumber: 11.2 Consensus size: 18
43906 TAATTTATAC
43916 TATAGTATATATAAACTA
1 TATAGTATATATAAACTA
*
43934 TATAATATATATAAACTA
1 TATAGTATATATAAACTA
**
43952 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
43968 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
*
43985 TATAATATATATAAACTA
1 TATAGTATATATAAACTA
*
44003 TATGGTATATATAAACTA
1 TATAGTATATATAAACTA
* * **
44021 TACATTATATAT-ATTTCA
1 TATAGTATATATAAACT-A
44039 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
* * *
44056 TATATTATATAGTTCATTAGTA
1 TATAGTATATA--T-A-AACTA
*
44078 TATA-TAAAGTATAAACTA
1 TATAGTATA-TATAAACTA
*
44096 TATAGTATATGTAAACTA
1 TATAGTATATATAAACTA
44114 TAT
1 TAT
44117 TAGTGTACTA
Statistics
Matches: 144, Mismatches: 25, Indels: 28
0.73 0.13 0.14
Matches are distributed among these distances:
15 4 0.03
16 8 0.06
17 20 0.14
18 93 0.65
19 4 0.03
20 2 0.01
21 4 0.03
22 9 0.06
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.42
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:43981 original size:33 final size:33
Alignment explanation
Indices: 43939--44101 Score: 193
Period size: 33 Copynumber: 4.8 Consensus size: 33
43929 AACTATATAA
43939 TATATATAAACTATATATTATATAGTTCATTAG
1 TATATATAAACTATATATTATATAGTTCATTAG
** *
43972 TATATATAAACTATATAATATATATA-AACTATATGG
1 TATATATAAACTATAT-AT-TATATAGTTC-AT-TAG
* *
44008 TATATATAAACTATACATTATATATATTTCATTAG
1 TATATATAAACTATATA-T-TATATAGTTCATTAG
44043 TATATATAAACTATATATTATATAGTTCATTAG
1 TATATATAAACTATATATTATATAGTTCATTAG
* * *
44076 TATATATAAAGTATAAACTATATAGT
1 TATATATAAACTATATATTATATAGT
44102 ATATGTAAAC
Statistics
Matches: 112, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
33 53 0.47
34 4 0.04
35 27 0.24
36 27 0.24
37 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (33 bp):
TATATATAAACTATATATTATATAGTTCATTAG
Found at i:44001 original size:69 final size:71
Alignment explanation
Indices: 43916--44066 Score: 234
Period size: 71 Copynumber: 2.2 Consensus size: 71
43906 TAATTTATAC
* *
43916 TATAGTATATATAAACTATATAATATATATAAACTATATA-T-TATATAGTTCATTAGTATATAT
1 TATAATATATATAAACTATATAATATATATAAACTATACATTATATATAGTTCATTAGTATATAT
43979 AAACTA
66 AAACTA
** *
43985 TATAATATATATAAACTATATGGTATATATAAACTATACATTATATATATTTCATTAGTATATAT
1 TATAATATATATAAACTATATAATATATATAAACTATACATTATATATAGTTCATTAGTATATAT
44050 AAACTA
66 AAACTA
*
44056 TATATTATATA
1 TATAATATATA
44067 GTTCATTAGT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
69 36 0.49
70 1 0.01
71 37 0.50
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (71 bp):
TATAATATATATAAACTATATAATATATATAAACTATACATTATATATAGTTCATTAGTATATAT
AAACTA
Found at i:44003 original size:104 final size:104
Alignment explanation
Indices: 43895--44099 Score: 256
Period size: 104 Copynumber: 2.0 Consensus size: 104
43885 ATATTTATGT
* * *
43895 ACTATATAAAATAATTTATACTATA-GTATATATAAACTAT-A-TAATATATATAAACTATATAT
1 ACTATATAAAAT-ATATAAACTATACAT-TATATAAA-TATCATTAATATATATAAACTATATAT
43957 TATATAGTTCATTAGTATATATAAACTATATAA-TATATATAA
63 TATATAGTTCATTAGTATATATAAACTATA-AACTATATATAA
*** * * *
43999 ACTATATGGTATATATAAACTATACATTATATATATTTCATTAGTATATATAAACTATATATTAT
1 ACTATATAAAATATATAAACTATACATTATATAAATATCATTAATATATATAAACTATATATTAT
*
44064 ATAGTTCATTAGTATATATAAAGTATAAACTATATA
66 ATAGTTCATTAGTATATATAAACTATAAACTATATA
44100 GTATATGTAA
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
102 2 0.02
103 20 0.23
104 65 0.75
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.42
Consensus pattern (104 bp):
ACTATATAAAATATATAAACTATACATTATATAAATATCATTAATATATATAAACTATATATTAT
ATAGTTCATTAGTATATATAAACTATAAACTATATATAA
Found at i:44258 original size:14 final size:14
Alignment explanation
Indices: 44241--44301 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
44231 TAATATATTA
44241 TATAGTTTATAAAC
1 TATAGTTTATAAAC
* * *
44255 TATACTATATTAA-
1 TATAGTTTATAAAC
* *
44268 TATTAATTATATTAAC
1 TA-TAGTT-TATAAAC
44284 TATAGTTTATAAAC
1 TATAGTTTATAAAC
44298 TATA
1 TATA
44302 CTATATAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
13 2 0.05
14 23 0.62
15 10 0.27
16 2 0.05
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (14 bp):
TATAGTTTATAAAC
Found at i:44267 original size:65 final size:64
Alignment explanation
Indices: 44195--44315 Score: 172
Period size: 65 Copynumber: 1.9 Consensus size: 64
44185 CTATATAGTT
* * * *
44195 TATATTAATGTTAATTATCTTAACTATAATTTATATTAA-TATATTATATAGTTTATAAACTATA
1 TATATTAATATTAATTATATTAACTATAATTTATA--AACTATACTATATAATTTATAAACTATA
44259 C
64 C
*
44260 TATATTAATATTAATTATATTAACTATAGTTTATAAACTATACTATATAATTTATA
1 TATATTAATATTAATTATATTAACTATAATTTATAAACTATACTATATAATTTATA
44316 TCATATAGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
63 2 0.04
64 16 0.32
65 32 0.64
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (64 bp):
TATATTAATATTAATTATATTAACTATAATTTATAAACTATACTATATAATTTATAAACTATAC
Found at i:44296 original size:43 final size:40
Alignment explanation
Indices: 44217--44329 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 40
44207 AATTATCTTA
*
44217 ACTATAATTTATATTAATATATTATATAGTTTATAAACTAT
1 ACTAT-ATTAATATTAATATATTATATAGTTTATAAACTAT
44258 ACTATATTAATATTAATTATATTAACTATAGTTTATAAACTAT
1 ACTATATTAATATTAA-TATATT-A-TATAGTTTATAAACTAT
*
44301 ACTATA-T-A-ATT--TATATCATATAGTTTATA
1 ACTATATTAATATTAATATATTATATAGTTTATA
44330 TTTTTATTAA
Statistics
Matches: 67, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
35 11 0.16
36 1 0.01
37 5 0.07
40 13 0.19
41 12 0.18
42 2 0.03
43 23 0.34
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (40 bp):
ACTATATTAATATTAATATATTATATAGTTTATAAACTAT
Found at i:44308 original size:14 final size:14
Alignment explanation
Indices: 44248--44309 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
44238 TTATATAGTT
44248 TATAAACTATACTA
1 TATAAACTATACTA
* *
44262 TATTAA-TATTAATTA
1 TATAAACTA-T-ACTA
* * *
44277 TATTAACTATAGTT
1 TATAAACTATACTA
44291 TATAAACTATACTA
1 TATAAACTATACTA
44305 TATAA
1 TATAA
44310 TTTATATCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 2 0.05
14 24 0.63
15 10 0.26
16 2 0.05
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.44
Consensus pattern (14 bp):
TATAAACTATACTA
Found at i:44443 original size:13 final size:12
Alignment explanation
Indices: 44419--44461 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 12
44409 AAGTTAATAT
44419 TAATATTAATTA
1 TAATATTAATTA
44431 TAATATATAATTA
1 TAATAT-TAATTA
44444 TTTTAATATTAATTA
1 ---TAATATTAATTA
44459 TAA
1 TAA
44462 ATAGTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 9 0.33
13 6 0.22
15 6 0.22
16 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATATTAATTA
Found at i:46606 original size:15 final size:15
Alignment explanation
Indices: 46586--46616 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
46576 AACCTTGTAA
46586 AACCTTAACTATAAG
1 AACCTTAACTATAAG
46601 AACCTTAACTATAAG
1 AACCTTAACTATAAG
46616 A
1 A
46617 TCTGAGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (15 bp):
AACCTTAACTATAAG
Found at i:46956 original size:13 final size:13
Alignment explanation
Indices: 46937--46974 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
46927 TAATTTAGTG
46937 ATTATAAATAA-A
1 ATTATAAATAAGA
46949 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
46964 ATTATAAATAA
1 ATTATAAATAA
46975 TATAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:46984 original size:19 final size:19
Alignment explanation
Indices: 46953--47070 Score: 72
Period size: 19 Copynumber: 6.5 Consensus size: 19
46943 AATAAAATTT
46953 ATAATAT-AAGAATTATAA
1 ATAATATAAAGAATTATAA
46971 ATAATATAAAGAATT-TGAA
1 ATAATATAAAGAATTAT-AA
* *
46990 TTAATATAAA-AATCA-AA
1 ATAATATAAAGAATTATAA
* * * * *
47007 TTTATAATACACAA--AT-T
1 ATAAT-ATAAAGAATTATAA
47024 ATAATAT-AAGAATTATAA
1 ATAATATAAAGAATTATAA
* *
47042 AAAATATAAAGAATTGTAA
1 ATAATATAAAGAATTATAA
*
47061 TTAATATAAA
1 ATAATATAAA
47071 AACTAAATTT
Statistics
Matches: 76, Mismatches: 14, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
15 3 0.04
16 2 0.03
17 12 0.16
18 21 0.28
19 38 0.50
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (19 bp):
ATAATATAAAGAATTATAA
Found at i:46997 original size:37 final size:36
Alignment explanation
Indices: 46954--47069 Score: 107
Period size: 37 Copynumber: 3.2 Consensus size: 36
46944 ATAAAATTTA
46954 TAATATAAGAATTATAAATAATATAAAGAATTTGAAT
1 TAATATAAGAATTATAAATAATATAAAGAA-TTGAAT
* * * *
46991 TAATATAAAAATCA-AATTTATAATACACA-AATT--A-
1 TAATATAAGAATTATAA---ATAATATAAAGAATTGAAT
*
47025 TAATATAAGAATTATAAAAAATATAAAGAATTGTAAT
1 TAATATAAGAATTATAAATAATATAAAGAATTG-AAT
47062 TAATATAA
1 TAATATAA
47070 AAACTAAATT
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
32 7 0.11
33 4 0.07
34 12 0.20
35 3 0.05
36 3 0.05
37 22 0.36
38 2 0.03
39 8 0.13
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.34
Consensus pattern (36 bp):
TAATATAAGAATTATAAATAATATAAAGAATTGAAT
Found at i:49853 original size:3 final size:3
Alignment explanation
Indices: 49845--49936 Score: 148
Period size: 3 Copynumber: 30.7 Consensus size: 3
49835 TAATGACCAT
* *
49845 GAA GAA GAA GAA GTA GAA GAA GAA GAA GTA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
49893 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAT GAT GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
49937 CACAGAAACT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.04
Consensus pattern (3 bp):
GAA
Found at i:54449 original size:20 final size:19
Alignment explanation
Indices: 54426--54478 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
54416 TTTTCTTATA
*
54426 TTTATATATTTTTTAATATT
1 TTTATATATTATTTAAT-TT
54446 TTTAT-TAATTATTTAATTT
1 TTTATAT-ATTATTTAATTT
* *
54465 TATATATATAATTT
1 TTTATATATTATTT
54479 TATAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATATATTATTTAATTT
Found at i:54457 original size:27 final size:26
Alignment explanation
Indices: 54421--54496 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 26
54411 TTAAATTTTC
* *
54421 TTATATTTATATATTTTTTAATATTT
1 TTATAATTATATATTTTTTAATAATT
*
54447 TTATTAATTATTTAATTTTATATATATAATT
1 TTA-TAATTATAT-ATTTT-T-TA-ATAATT
54478 TTATAA-TATA-ATTTTTTAA
1 TTATAATTATATATTTTTTAA
54497 GTTCATGCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
24 1 0.02
25 2 0.05
26 4 0.10
27 12 0.29
28 5 0.12
29 4 0.10
30 5 0.12
31 8 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
TTATAATTATATATTTTTTAATAATT
Found at i:54495 original size:15 final size:14
Alignment explanation
Indices: 54459--54492 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
54449 ATTAATTATT
54459 TAATTTTATATATA
1 TAATTTTATATATA
54473 TAATTTTATA-ATA
1 TAATTTTATATATA
54486 TAATTTT
1 TAATTTT
54493 TTAAGTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTTTATATATA
Found at i:54592 original size:15 final size:15
Alignment explanation
Indices: 54574--54603 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54564 AGTTGAATTC
54574 AGGTACGGTATTTTA
1 AGGTACGGTATTTTA
*
54589 AGGTAGGGTATTTTA
1 AGGTACGGTATTTTA
54604 GGCTTTCCGG
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:0.27, C:0.03, G:0.30, T:0.40
Consensus pattern (15 bp):
AGGTACGGTATTTTA
Found at i:56961 original size:22 final size:22
Alignment explanation
Indices: 56917--56966 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
56907 CTATATTTAT
*
56917 TATTTATTTAATGACTATAGGA
1 TATTTAATTAATGACTATAGGA
* *
56939 TTTTTAATTAAT-ACTAGTCGGA
1 TATTTAATTAATGACTA-TAGGA
56961 TATTTA
1 TATTTA
56967 CGCGATTGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (22 bp):
TATTTAATTAATGACTATAGGA
Found at i:61635 original size:2 final size:2
Alignment explanation
Indices: 61628--61662 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
61618 ATCCAATTAA
61628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61663 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61667 original size:2 final size:2
Alignment explanation
Indices: 61662--61700 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
61652 ATATATATAT
61662 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
61701 AAGGAAGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.