Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003688.1 Hibiscus syriacus cultivar Beakdansim tig00007877_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: 61386
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:8621 original size:18 final size:18
Alignment explanation
Indices: 8598--8692 Score: 100
Period size: 18 Copynumber: 4.9 Consensus size: 18
8588 ACTGAATATT
8598 TATCCCGAAGGACCACTA
1 TATCCCGAAGGACCACTA
*
8616 TATCCCCAAGGACCACTAA
1 TATCCCGAAGGACCACT-A
* *
8635 TTATTCCGAAGAACCACTA
1 -TATCCCGAAGGACCACTA
*
8654 TGTCCCGAAGGACCACTGTA
1 TATCCCGAAGGACCAC--TA
8674 TATGTCCCGAAGGACCACT
1 TA--TCCCGAAGGACCACT
8693 CCTTAAGAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
18 29 0.46
19 2 0.03
20 18 0.29
22 14 0.22
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.20
Consensus pattern (18 bp):
TATCCCGAAGGACCACTA
Found at i:8645 original size:38 final size:37
Alignment explanation
Indices: 8597--8692 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 37
8587 CACTGAATAT
*
8597 TTATCCCGAAGGACCACTATATCCCCAAGGACCACTAA
1 TTATTCCGAAGGACCACTATATCCCCAAGGACCACT-A
* * * *
8635 TTATTCCGAAGAACCACTATGTCCCGAAGGACCACTG
1 TTATTCCGAAGGACCACTATATCCCCAAGGACCACTA
8672 TATATGTCCCGAAGGACCACT
1 T-TAT-T-CCGAAGGACCACT
8693 CCTTAAGAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
37 1 0.02
38 35 0.71
39 1 0.02
40 12 0.24
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (37 bp):
TTATTCCGAAGGACCACTATATCCCCAAGGACCACTA
Found at i:9463 original size:19 final size:19
Alignment explanation
Indices: 9441--9485 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
9431 AGGTGCATTG
9441 ATGCACTCCTCATGCATCA
1 ATGCACTCCTCATGCATCA
*
9460 ATGCACTCCTCATGCATCG
1 ATGCACTCCTCATGCATCA
9479 ATGCACT
1 ATGCACT
9486 AATTGCATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.24, C:0.36, G:0.13, T:0.27
Consensus pattern (19 bp):
ATGCACTCCTCATGCATCA
Found at i:9538 original size:21 final size:21
Alignment explanation
Indices: 9509--9551 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9499 GTTCAATGTT
*
9509 TTGATTGTGCATCGATACACA
1 TTGAATGTGCATCGATACACA
*
9530 TTGAATGTGCATCGATGCACA
1 TTGAATGTGCATCGATACACA
9551 T
1 T
9552 AACCTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (21 bp):
TTGAATGTGCATCGATACACA
Found at i:15623 original size:18 final size:18
Alignment explanation
Indices: 15600--15692 Score: 60
Period size: 18 Copynumber: 4.8 Consensus size: 18
15590 TGAATATTTG
15600 TCCCGAAGGACCACTATA
1 TCCCGAAGGACCACTATA
* * *
15618 TCCCGAAGGACTATTGATTG
1 TCCCGAAGGACCACT-A-TA
* * * *
15638 TTCCGGAGAACCACTATG
1 TCCCGAAGGACCACTATA
*
15656 TTCCGAAGGACCACTGTATA
1 TCCCGAAGGACCAC--TATA
15676 TGTCCCGAAGGACCACT
1 --TCCCGAAGGACCACT
15693 CCTTAAGAAC
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
18 27 0.47
19 2 0.04
20 15 0.26
22 13 0.23
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (18 bp):
TCCCGAAGGACCACTATA
Found at i:24033 original size:17 final size:17
Alignment explanation
Indices: 24013--24051 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
24003 ATTTCAAAGT
24013 TATAATTATATAAAAAA
1 TATAATTATATAAAAAA
* *
24030 TATATTTATATATAAAA
1 TATAATTATATAAAAAA
24047 TATAA
1 TATAA
24052 ATAAAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAATTATATAAAAAA
Found at i:24317 original size:2 final size:2
Alignment explanation
Indices: 24312--24343 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
24302 TAATAAAAAA
24312 AT AT AT AT -T AT -T 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 AT AT
24344 TTTATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:24364 original size:3 final size:3
Alignment explanation
Indices: 24350--24413 Score: 55
Period size: 3 Copynumber: 22.3 Consensus size: 3
24340 ATATTTTATA
* * * *
24350 AAT AAT AA- AAT AAT AAT AAT GA- AAT AAT AATT AA- AAA AAA AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
24393 AAT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
24414 TTGCAAATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
2 7 0.13
3 43 0.81
4 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:24369 original size:14 final size:14
Alignment explanation
Indices: 24350--24413 Score: 70
Period size: 14 Copynumber: 5.1 Consensus size: 14
24340 ATATTTTATA
24350 AATAATAAAATAAT
1 AATAATAAAATAAT
*
24364 AATAATGAAATAAT
1 AATAATAAAATAAT
24378 AAT--T-AAA-AA-
1 AATAATAAAATAAT
24387 AA-AA-AAAATAAT
1 AATAATAAAATAAT
24399 AATAATAAAATAAT
1 AATAATAAAATAAT
24413 A
1 A
24414 TTGCAAATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
9 2 0.05
10 5 0.12
11 5 0.12
12 3 0.07
13 2 0.05
14 25 0.60
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
AATAATAAAATAAT
Found at i:25671 original size:3 final size:3
Alignment explanation
Indices: 25665--25709 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
25655 TTTTTTTATT
* *
25665 TAA TAA TAA TAA TAA TAA TAC TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25710 AACGAAATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:26257 original size:76 final size:76
Alignment explanation
Indices: 25884--26661 Score: 1130
Period size: 76 Copynumber: 10.4 Consensus size: 76
25874 GAAGTCTTAT
* * * * **
25884 CATCTTGCACTGTAGGTCTTACAGATGACCCTGAGGCTTT---AAGATCAAAAAGCTCTTGAAGG
1 CATCATGCACTGTAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGG
* *
25946 TTTTTTTTGAAAA
66 --CTTTTTGGAAA
* ** * *
25959 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGACTTT---AAGATCAAAAAGCTCCCGAAGA
1 CATCATGCACTGTAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGG
*
26021 CTTTTTGAAAA
66 CTTTTTGGAAA
* * * * *
26032 CATCATGCACTGTAGGTCTTACAGGTGACCCAGA-GGTTT--TAAGATCAAAAAGCTCCCGAAGG
1 CATCATGCACTGTAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGG
26094 CTTTTTGGAAA
66 CTTTTTGGAAA
* *
26105 CATCATGCACTGTAGGACTTACAGATGACCCTGA-GGTTT--TAAGATCAAAAAGCTCCCGAAGG
1 CATCATGCACTGTAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGG
*
26167 CTTTTTGAAAA
66 CTTTTTGGAAA
* * *
26178 CATCATGAACTGTAGGTCTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTTCCGAAGG
1 CATCATGCACTGTAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGG
26243 CTTTTTGGAAA
66 CTTTTTGGAAA
* *
26254 CATCATGCACTGTAGGACTTACATATGACCCTGAGGGTTTGAAAACATCAAAAAGCTACCGAAGG
1 CATCATGCACTGTAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGG
26319 CTTTTTGGAAA
66 CTTTTTGGAAA
* *
26330 CATCATACACTATAGGACTTACAGATGACCCTGAGGGTTTTGAAAACATCAAAAAGCTCCCGAAG
1 CATCATGCACTGTAGGACTTACAGATGACCCTGAGGG-TTTGAAAACATCAAAAAGCTCCCGAAG
26395 GCTTTTTGGAAA
65 GCTTTTTGGAAA
* *
26407 CATCATGCACTGCAGGACTTACAGATGACCATGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGG
1 CATCATGCACTGTAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGG
26472 CTTTTTGGAAA
66 CTTTTTGGAAA
*
26483 CATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGG
1 CATCATGCACTGTAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGG
26548 CTTTTTGGAAA
66 CTTTTTGGAAA
*
26559 CATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGG
1 CATCATGCACTGTAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGG
*
26624 CTTTTTTGAAA
66 CTTTTTGGAAA
*
26635 CATCATGCACTGCAGGACTTACAGATG
1 CATCATGCACTGTAGGACTTACAGATG
26662 TGAGAAATAG
Statistics
Matches: 662, Mismatches: 36, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
72 3 0.00
73 174 0.26
74 5 0.01
75 57 0.09
76 352 0.53
77 71 0.11
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (76 bp):
CATCATGCACTGTAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGG
CTTTTTGGAAA
Found at i:26447 original size:229 final size:225
Alignment explanation
Indices: 25884--26661 Score: 1120
Period size: 229 Copynumber: 3.4 Consensus size: 225
25874 GAAGTCTTAT
* * * * ** *
25884 CATCTTGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCTTGAAGGTTT
1 CATCATGCACTGTAGGACTTACAGATGACCCTGAGGTTTTAACATCAAAAAGCTCCCGAAGG--C
* * ** *
25949 TTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGACTTT---AAGATCAAAAAG
64 TTTTTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAG
* * * * * *
26011 CTCCCGAAGACTTTTTGAAAACATCATGCACTGTAGGTCTTACAGGTGACCCAGA-GGTTT--TA
129 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTGAGGGTTTGAAA
*
26073 AGATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
194 ACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
*
26105 CATCATGCACTGTAGGACTTACAGATGACCCTGAGGTTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGACTTACAGATGACCCTGAGGTTTTAACATCAAAAAGCTCCCGAAGGCTT
* * *
26170 TTTGAAAACATCATGAACTGTAGGTCTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCT
66 TTTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCT
* *
26235 TCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACATATGACCCTGAGGGTTTGAAAAC
131 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTGAGGGTTTGAAAAC
*
26300 ATCAAAAAGCTACCGAAGGCTTTTTGGAAA
196 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
* *
26330 CATCATACACTATAGGACTTACAGATGACCCTGAGGGTTTTGAAAACATCAAAAAGCTCCCGAAG
1 CATCATGCACTGTAGGACTTACAGATGACCCTGA-GGTTTT---AACATCAAAAAGCTCCCGAAG
* *
26395 GCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCATGAGGGTTTGAAAACATCAAAA
62 GCTTTTTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAA
*
26460 AGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGA
127 AGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTGAGGGTTTGA
26525 AAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
192 AAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
* *
26559 CATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGG
1 CATCATGCACTGTAGGACTTACAGATGACCCTGA-GGTTT--TAACATCAAAAAGCTCCCGAAGG
26624 CTTTTTTG-AAACATCATGCACTGCAGGACTTACAGATG
63 C-TTTTTGAAAACATCATGCACTGCAGGACTTACAGATG
26662 TGAGAAATAG
Statistics
Matches: 508, Mismatches: 36, Indels: 19
0.90 0.06 0.03
Matches are distributed among these distances:
219 47 0.09
221 57 0.11
222 59 0.12
223 5 0.01
225 63 0.12
226 6 0.01
228 53 0.10
229 218 0.43
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (225 bp):
CATCATGCACTGTAGGACTTACAGATGACCCTGAGGTTTTAACATCAAAAAGCTCCCGAAGGCTT
TTTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTGAGGGTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
Found at i:26958 original size:185 final size:186
Alignment explanation
Indices: 26602--26958 Score: 644
Period size: 185 Copynumber: 1.9 Consensus size: 186
26592 AGGGTTTGAA
* *
26602 AACATCAAAAAGCTCCCGAAGGCTTTTTTGAAACATCATGCACTGCAGGACTTACAGATGTGAGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATATGAGA
26667 AATAGTTTACTAAGTAAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTT
66 AATAGTTTACTAAGT-AAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTT
*
26732 AGAAAAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAGTAAC
130 AGAAAAGATTGAATGAGAAACTATGAAAATCATTTTCTCATTATTTTTCAAAGTAAC
*
26789 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATATGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATATGAGA
26854 AATAGTTTACTAAGT-AAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
66 AATAGTTTACTAAGTAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
* *
26918 GAAAAGATTGAATGATAAACTATGGAAATCATTTTCTCATT
131 GAAAAGATTGAATGAGAAACTATGAAAATCATTTTCTCATT
26959 CTGTTTTTGA
Statistics
Matches: 164, Mismatches: 6, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
185 87 0.53
187 77 0.47
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (186 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATATGAGA
AATAGTTTACTAAGTAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
GAAAAGATTGAATGAGAAACTATGAAAATCATTTTCTCATTATTTTTCAAAGTAAC
Found at i:27551 original size:22 final size:22
Alignment explanation
Indices: 27526--27584 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
27516 CATAAAGCTT
27526 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
27548 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
27570 TCATCTTTGCAAAGA
1 TCATCTTTGAAAAGA
27585 AGTCTCTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:31731 original size:73 final size:73
Alignment explanation
Indices: 31529--31808 Score: 280
Period size: 73 Copynumber: 3.8 Consensus size: 73
31519 AACAAATCAA
* *
31529 AGCTTAAATTAAGGAAACAAGTGGGGGAAACAAATACTATAATAA-TTCTATATATATTATTAAT
1 AGCTTAAATTAAGGAAACAAGT-GGGGAAACAAATATTATAATAACTTC---ATATATTA--AAA
*
31593 AACTAAACACCAAACAT
60 AACT-AA-ACC-AATAT
* * * *
31610 AGCTTAAATTAAGG--A-AAGTGGAGAAACCAATATTATAATAATTTCATATATTAAAAAAGTAA
1 AGCTTAAATTAAGGAAACAAGTGGGGAAACAAATATTATAATAACTTCATATATTAAAAAACTAA
*
31672 ACCATTAT
66 ACCAATAT
* * * * *
31680 AACTTAAATTAAGGAAACATGTGGGGAAACAAATAATATAATGACTCCATATATTAAAAAACTAA
1 AGCTTAAATTAAGGAAACAAGTGGGGAAACAAATATTATAATAACTTCATATATTAAAAAACTAA
*
31745 ACCACTAT
66 ACCAATAT
* * * * *
31753 TGCTTAAATTAAGGACACAAGTGGGAAAACAAATATTATAATGATTTCATATATTA
1 AGCTTAAATTAAGGAAACAAGTGGGGAAACAAATATTATAATAACTTCATATATTA
31809 TGTTTTTTTT
Statistics
Matches: 170, Mismatches: 25, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
70 16 0.09
71 3 0.02
72 3 0.02
73 99 0.58
75 8 0.05
77 19 0.11
78 7 0.04
79 1 0.01
81 14 0.08
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (73 bp):
AGCTTAAATTAAGGAAACAAGTGGGGAAACAAATATTATAATAACTTCATATATTAAAAAACTAA
ACCAATAT
Found at i:31794 original size:146 final size:148
Alignment explanation
Indices: 31531--31808 Score: 354
Period size: 146 Copynumber: 1.9 Consensus size: 148
31521 CAAATCAAAG
* * *
31531 CTTAAATTAAGGAAACAAGTGGGGGAAACAAATACTATAATAATTCTATATATATTATTAATAAC
1 CTTAAATTAAGGAAACAAGTGGGGGAAACAAATAATATAATAA-TCTACATATATTA-TAAAAAC
*
31596 TAAACACCAAACATAGCTTAAATTAAGGAAAGTGGAGAAACCAATATTATAATAATTTCATATAT
64 TAAACACC-AACATAGCTTAAATTAAGGAAAGTGGAGAAACAAATATTATAATAATTTCATATAT
31661 TAAAAAAGTAAACCATTATAA
128 TAAAAAAGTAAACCATTATAA
* * *
31682 CTTAAATTAAGGAAACATGT-GGGGAAACAAATAATATAATGA-CTCCATATATTA-AAAAACT-
1 CTTAAATTAAGGAAACAAGTGGGGGAAACAAATAATATAATAATCTACATATATTATAAAAACTA
* *
31743 AA-ACC-ACTATTGCTTAAATTAAGGACACAAGTGG-GAAAACAAATATTATAATGATTTCATAT
66 AACACCAAC-ATAGCTTAAATTAAGG--A-AAGTGGAG-AAACAAATATTATAATAATTTCATAT
31805 ATTA
126 ATTA
31809 TGTTTTTTTT
Statistics
Matches: 113, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
142 2 0.02
143 15 0.13
144 3 0.03
145 4 0.04
146 40 0.35
148 10 0.09
150 20 0.18
151 19 0.17
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (148 bp):
CTTAAATTAAGGAAACAAGTGGGGGAAACAAATAATATAATAATCTACATATATTATAAAAACTA
AACACCAACATAGCTTAAATTAAGGAAAGTGGAGAAACAAATATTATAATAATTTCATATATTAA
AAAAGTAAACCATTATAA
Found at i:33080 original size:26 final size:26
Alignment explanation
Indices: 33048--33143 Score: 83
Period size: 24 Copynumber: 3.8 Consensus size: 26
33038 TGGTAGCAGT
*
33048 GGTGGCTATTGAGTGGTCCAAGAGGC
1 GGTGGCTATTGAGTGGTCCAAGCGGC
* * *
33074 GGTGGCTGTT--CTGGTCCAAGCGGT
1 GGTGGCTATTGAGTGGTCCAAGCGGC
* * *
33098 GGTGGCTGTCGAATGGTCCAAGCGGC
1 GGTGGCTATTGAGTGGTCCAAGCGGC
* *
33124 AGTGGC-A-TGAGTGGTTCAAG
1 GGTGGCTATTGAGTGGTCCAAG
33144 TGGTTGCGGC
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
24 30 0.54
26 26 0.46
ACGTcount: A:0.17, C:0.18, G:0.42, T:0.24
Consensus pattern (26 bp):
GGTGGCTATTGAGTGGTCCAAGCGGC
Found at i:33379 original size:15 final size:16
Alignment explanation
Indices: 33356--33385 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33346 AAAATAAAAT
33356 ATAATTATAAATAATA
1 ATAATTATAAATAATA
33372 ATAA-TATAAATAAT
1 ATAATTATAAATAAT
33386 GATGAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAATTATAAATAATA
Found at i:46601 original size:18 final size:18
Alignment explanation
Indices: 46578--46672 Score: 100
Period size: 18 Copynumber: 4.9 Consensus size: 18
46568 ACTGAATATT
46578 TATCCCGAAGGACCACTA
1 TATCCCGAAGGACCACTA
*
46596 TATCCCCAAGGACCACTAA
1 TATCCCGAAGGACCACT-A
* *
46615 TTATTCCGAAGAACCACTA
1 -TATCCCGAAGGACCACTA
*
46634 TGTCCCGAAGGACCACTGTA
1 TATCCCGAAGGACCAC--TA
46654 TATGTCCCGAAGGACCACT
1 TA--TCCCGAAGGACCACT
46673 CCTTAAGAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
18 29 0.46
19 2 0.03
20 18 0.29
22 14 0.22
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.20
Consensus pattern (18 bp):
TATCCCGAAGGACCACTA
Found at i:46625 original size:38 final size:37
Alignment explanation
Indices: 46577--46672 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 37
46567 CACTGAATAT
*
46577 TTATCCCGAAGGACCACTATATCCCCAAGGACCACTAA
1 TTATTCCGAAGGACCACTATATCCCCAAGGACCACT-A
* * * *
46615 TTATTCCGAAGAACCACTATGTCCCGAAGGACCACTG
1 TTATTCCGAAGGACCACTATATCCCCAAGGACCACTA
46652 TATATGTCCCGAAGGACCACT
1 T-TAT-T-CCGAAGGACCACT
46673 CCTTAAGAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
37 1 0.02
38 35 0.71
39 1 0.02
40 12 0.24
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (37 bp):
TTATTCCGAAGGACCACTATATCCCCAAGGACCACTA
Found at i:47441 original size:19 final size:19
Alignment explanation
Indices: 47419--47463 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
47409 AGGTGCATTG
47419 ATGCACTCCTCATGCATCA
1 ATGCACTCCTCATGCATCA
*
47438 ATGCACTCCTCATGCATCG
1 ATGCACTCCTCATGCATCA
47457 ATGCACT
1 ATGCACT
47464 AATTGCATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.24, C:0.36, G:0.13, T:0.27
Consensus pattern (19 bp):
ATGCACTCCTCATGCATCA
Found at i:47516 original size:21 final size:21
Alignment explanation
Indices: 47487--47529 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
47477 GTTCAATGTT
*
47487 TTGATTGTGCATCGATACACA
1 TTGAATGTGCATCGATACACA
*
47508 TTGAATGTGCATCGATGCACA
1 TTGAATGTGCATCGATACACA
47529 T
1 T
47530 AACCTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (21 bp):
TTGAATGTGCATCGATACACA
Found at i:53629 original size:18 final size:18
Alignment explanation
Indices: 53606--53640 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53596 GGACCTTGAT
*
53606 TGTTCCGGAGAACCACTA
1 TGTTCCGAAGAACCACTA
*
53624 TGTTCCGAAGGACCACT
1 TGTTCCGAAGAACCACT
53641 GTATATGTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (18 bp):
TGTTCCGAAGAACCACTA
Found at i:53913 original size:24 final size:21
Alignment explanation
Indices: 53857--53914 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
53847 ATATCTTCTC
53857 ATCACTTTTCATATAAACATGT
1 ATCAC-TTTCATATAAACATGT
53879 ATTTCAC-TTCATATACACACATGT
1 A--TCACTTTCATATA-A-ACATGT
53903 GATCACTTTCAT
1 -ATCACTTTCAT
53915 TATTTCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 9 0.30
23 5 0.17
24 15 0.50
25 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (21 bp):
ATCACTTTCATATAAACATGT
Found at i:58459 original size:10 final size:10
Alignment explanation
Indices: 58444--58474 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
58434 GCACTGTATT
58444 TTTAGTTGCA
1 TTTAGTTGCA
58454 TTTAGTTGCA
1 TTTAGTTGCA
58464 TTTAGTTGCA
1 TTTAGTTGCA
58474 T
1 T
58475 ATAGGTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (10 bp):
TTTAGTTGCA
Done.