Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005413.1 Hibiscus syriacus cultivar Beakdansim tig00012411_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: 60114
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:14193 original size:42 final size:41
Alignment explanation
Indices: 14140--14380 Score: 192
Period size: 41 Copynumber: 5.9 Consensus size: 41
14130 AAAATGAAAC
* * *
14140 TTTAGCGGCGTTTTT-TCAACAAACGCCGCAATAGGGTGGTAA
1 TTTAGCGGCGTTTTTAT--ATAAACGCCGCAATAGAGTAGTAA
* *
14182 TTTAGCTGCGTTTTTATATAAACGCCGCAATAGAGTTGT--
1 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTAGTAA
* * * * *
14221 TTATAGTGACGTTTTCTAAAAAAACACCGCAATAGAGTAGTAA
1 TT-TAGCGGCGTTTT-TATATAAACGCCGCAATAGAGTAGTAA
*
14264 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGT--
1 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTAGTAA
* * * * *
14303 TTATAGTGGCG-TTTTACAAGAAACGCCGCAA-ATGGGTCGTACA
1 TT-TAGCGGCGTTTTTA-TATAAACGCCGCAATA-GAGTAGTA-A
* *
14346 -TTAGTGGCGTTTTTATATAAATGCCGCAATAGAGT
1 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGT
14381 TGCTTATAGT
Statistics
Matches: 160, Mismatches: 26, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
39 10 0.06
40 33 0.21
41 83 0.52
42 31 0.19
43 3 0.02
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTAGTAA
Found at i:14382 original size:81 final size:81
Alignment explanation
Indices: 14146--14456 Score: 373
Period size: 81 Copynumber: 3.8 Consensus size: 81
14136 AAACTTTAGC
* * *
14146 GGCGTTTTTTCAACAAACGCCGCAATAGGGTGGTAATTTAGCT-GCGTTTTTATATAAACGCCGC
1 GGCG-TTTTACAAGAAACGCCGCAATAGGGTCGTAATTTAG-TGGCGTTTTTATATAAACGCCGC
14210 AATAGAGTTGTTTATAGT
64 AATAGAGTTGTTTATAGT
* * * * * *
14228 GACGTTTT-CTAAAAAAACACCGCAATAGAGTAGTAATTTAGCGGCGTTTTTATATAAACGCCGC
1 GGCGTTTTAC--AAGAAACGCCGCAATAGGGTCGTAATTTAGTGGCGTTTTTATATAAACGCCGC
14292 AATAGAGTTGTTTATAGT
64 AATAGAGTTGTTTATAGT
*
14310 GGCGTTTTACAAGAAACGCCGCAA-ATGGGTCGTACA-TTAGTGGCGTTTTTATATAAATGCCGC
1 GGCGTTTTACAAGAAACGCCGCAATA-GGGTCGTA-ATTTAGTGGCGTTTTTATATAAACGCCGC
*
14373 AATAGAGTTGCTTATAGT
64 AATAGAGTTGTTTATAGT
* * * *
14391 GTCGTTTTACAAGAAACGCCGCAA-ATGGGTCGTACA-TTAGTAGCGTTTTTCTGTAAACGCCGC
1 GGCGTTTTACAAGAAACGCCGCAATA-GGGTCGTA-ATTTAGTGGCGTTTTTATATAAACGCCGC
14454 AAT
64 AAT
14457 TGATTTTAAC
Statistics
Matches: 204, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
80 2 0.01
81 125 0.61
82 76 0.37
83 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.32
Consensus pattern (81 bp):
GGCGTTTTACAAGAAACGCCGCAATAGGGTCGTAATTTAGTGGCGTTTTTATATAAACGCCGCAA
TAGAGTTGTTTATAGT
Found at i:14449 original size:41 final size:40
Alignment explanation
Indices: 14323--14455 Score: 112
Period size: 41 Copynumber: 3.3 Consensus size: 40
14313 GTTTTACAAG
* *
14323 AAACGCCGCAAATGGGTCGTACATTAGTGGCGTTTTTATAT
1 AAACGCCGCAAATGGGTCGTACATTAGT-GCGTTTTTCTGT
* * * * * *
14364 AAATGCCGC-AATAGAGT--TGCTTATAGTGTCGTTTTACAAG-
1 AAACGCCGCAAAT-GGGTCGTACAT-TAGTG-CGTTTTTC-TGT
14404 AAACGCCGCAAATGGGTCGTACATTAGTAGCGTTTTTCTGT
1 AAACGCCGCAAATGGGTCGTACATTAGT-GCGTTTTTCTGT
14445 AAACGCCGCAA
1 AAACGCCGCAA
14456 TTGATTTTAA
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
39 4 0.06
40 25 0.36
41 36 0.52
42 4 0.06
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (40 bp):
AAACGCCGCAAATGGGTCGTACATTAGTGCGTTTTTCTGT
Found at i:16005 original size:43 final size:43
Alignment explanation
Indices: 15923--16142 Score: 174
Period size: 43 Copynumber: 5.1 Consensus size: 43
15913 CTAAAATTTT
* *
15923 GTTTGTAGG-AAAACGCCGCTAAATATCAACATCTTCTGCGGC
1 GTTTGTAGGAAAAACGCCGCTAAAAATCAACATCTACTGCGGC
* * *
15965 GTTTGTAGGAAAAACGCCGGTAAAAATAAAAATCTACTGCGGC
1 GTTTGTAGGAAAAACGCCGCTAAAAATCAACATCTACTGCGGC
* * * *
16008 GTTTGT-GAAGAAAACGCCGCTAAACATCAACACCTATTGCGGC
1 GTTTGTAGGA-AAAACGCCGCTAAAAATCAACATCTACTGCGGC
** ** * * * * * *
16051 GTTTGTCTGCCAAATGCCGTTAAATATCAACACCTATTGCGGT
1 GTTTGTAGGAAAAACGCCGCTAAAAATCAACATCTACTGCGGC
* ** * * * **
16094 GTTTTTCTGAAAAACGCCGCTAAATATCAATACCTTTTGCGGC
1 GTTTGTAGGAAAAACGCCGCTAAAAATCAACATCTACTGCGGC
16137 GTTTGT
1 GTTTGT
16143 TGACGCCGCT
Statistics
Matches: 146, Mismatches: 29, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
42 11 0.08
43 135 0.92
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (43 bp):
GTTTGTAGGAAAAACGCCGCTAAAAATCAACATCTACTGCGGC
Found at i:16092 original size:86 final size:85
Alignment explanation
Indices: 15923--16142 Score: 221
Period size: 86 Copynumber: 2.6 Consensus size: 85
15913 CTAAAATTTT
* *
15923 GTTTGT-AGGAAAACGCCGCTAAATATCAACATCTTCTGCGGCGTTTGTAGGAAAAACGCCGGTA
1 GTTTGTGAAGAAAACGCCGCTAAATATCAACACCTT-TGCGGCGTTTGTAGGAAAAACGCCGGTA
*
15987 AAAATAAAAATCTACTGCGGC
65 AAAATAAAAACCTACTGCGGC
* ** ** * *
16008 GTTTGTGAAGAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCTGCCAAATGCCGTTA
1 GTTTGTGAAGAAAACGCCGCTAAATATCAACACCT-TTGCGGCGTTTGTAGGAAAAACGCCGGTA
* * * * *
16073 AATATCAACACCTATTGCGGT
65 AAAATAAAAACCTACTGCGGC
* *
16094 GTTTTTCTG-A-AAAACGCCGCTAAATATCAATACCTTTTGCGGCGTTTGT
1 G--TTTGTGAAGAAAACGCCGCTAAATATCAACACC-TTTGCGGCGTTTGT
16143 TGACGCCGCT
Statistics
Matches: 112, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
85 6 0.05
86 98 0.88
87 3 0.03
88 5 0.04
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (85 bp):
GTTTGTGAAGAAAACGCCGCTAAATATCAACACCTTTGCGGCGTTTGTAGGAAAAACGCCGGTAA
AAATAAAAACCTACTGCGGC
Found at i:18060 original size:19 final size:19
Alignment explanation
Indices: 18036--18089 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 19
18026 AAATAATTTT
18036 AAGAAAAAAATCAAGTTAA
1 AAGAAAAAAATCAAGTTAA
18055 AAGAAAAAAAAAATCAAGTTAA
1 AAG---AAAAAAATCAAGTTAA
*
18077 AAGATAAAAATCA
1 AAGAAAAAAATCA
18090 GCCTAGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 12 0.39
22 19 0.61
ACGTcount: A:0.70, C:0.06, G:0.09, T:0.15
Consensus pattern (19 bp):
AAGAAAAAAATCAAGTTAA
Found at i:18067 original size:22 final size:22
Alignment explanation
Indices: 18039--18086 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
18029 TAATTTTAAG
18039 AAAAAAATCAAGTTAAAAGAAA
1 AAAAAAATCAAGTTAAAAGAAA
*
18061 AAAAAAATCAAGTTAAAAGATA
1 AAAAAAATCAAGTTAAAAGAAA
18083 AAAA
1 AAAA
18087 TCAGCCTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.15
Consensus pattern (22 bp):
AAAAAAATCAAGTTAAAAGAAA
Found at i:18767 original size:21 final size:19
Alignment explanation
Indices: 18743--18781 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
18733 CATGAATTAA
18743 GGAAAATAAAGAAAAAAATTT
1 GGAAAA-AAA-AAAAAAATTT
*
18764 GGAAAAAGAAAAAAAATT
1 GGAAAAAAAAAAAAAATT
18782 ATAAACCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (19 bp):
GGAAAAAAAAAAAAAATTT
Found at i:20253 original size:56 final size:56
Alignment explanation
Indices: 20185--20301 Score: 225
Period size: 56 Copynumber: 2.1 Consensus size: 56
20175 GCTACTTTAG
20185 ATTTTAGATATGACATGAGTGATTTCATTATTCAGGCAATCAGAGAAATTTTAGAA
1 ATTTTAGATATGACATGAGTGATTTCATTATTCAGGCAATCAGAGAAATTTTAGAA
*
20241 ATTTTAGATATGACATGAGTGATTTCATTATTCAGGCAATCAGAGAAATTTTAGGA
1 ATTTTAGATATGACATGAGTGATTTCATTATTCAGGCAATCAGAGAAATTTTAGAA
20297 ATTTT
1 ATTTT
20302 GGTTTCTCAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (56 bp):
ATTTTAGATATGACATGAGTGATTTCATTATTCAGGCAATCAGAGAAATTTTAGAA
Found at i:28129 original size:21 final size:21
Alignment explanation
Indices: 28079--28130 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
28069 GAAGCTTTAA
*
28079 GATCATCAATTTCCTTTTGAT
1 GATCATCATTTTCCTTTTGAT
28100 GATCATCATTTTCCTTTTGAT
1 GATCATCATTTTCCTTTTGAT
28121 GATCATCATT
1 GATCATCATT
28131 GAACTTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (21 bp):
GATCATCATTTTCCTTTTGAT
Found at i:28137 original size:21 final size:21
Alignment explanation
Indices: 28092--28137 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
28082 CATCAATTTC
***
28092 CTTTTGATGATCATCATTTTC
1 CTTTTGATGATCATCATTGAA
28113 CTTTTGATGATCATCATTGAA
1 CTTTTGATGATCATCATTGAA
28134 CTTT
1 CTTT
28138 GAAAGTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (21 bp):
CTTTTGATGATCATCATTGAA
Found at i:31248 original size:20 final size:20
Alignment explanation
Indices: 31219--31261 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
31209 ATTCCACCAC
31219 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
31239 ATGCATCTATGTGGTCCTAA
1 ATGCAACTATATGCTCCTAA
31259 ATG
1 ATG
31262 AGCTCTTAGA
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:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:38993 original size:20 final size:20
Alignment explanation
Indices: 38964--39006 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
38954 ATTCCATCAC
38964 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
38984 ATGCATCTATGTGGTCCTAA
1 ATGCAACTATATGCTCCTAA
39004 ATG
1 ATG
39007 AGCTCTTAGA
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:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:39508 original size:803 final size:804
Alignment explanation
Indices: 38216--39826 Score: 2693
Period size: 803 Copynumber: 2.0 Consensus size: 804
38206 ATAGGATTAG
38216 TTCATGGTGGGGTTCGAAATAAACAAGCACAAGTCAAGTTTAATTCGTTCCTTACAACCCAATAA
1 TTCATGGTGGGGTTCGAAATAAACAAGCACAAGTCAAGTTTAATTCGTTCCTTACAACCCAATAA
*
38281 CAAAATATGAAAGCAAATAACTAAGGGAATGAGGAAAAGCCTTCGACGTGCACTGCTAGAGCTTC
66 CAAAATATGAAAGCAAAAAACTAAGGGAATGAGGAAAAGCCTTCGACGTGCACTGCTAGAGCTTC
*
38346 CCTTGGTCACCACAAACTGCCCCCAATGAACTAGCTCCTCTCGGATGACTTAGAACGCCACTCCT
131 CCTTGGTCACCACAAACTGCCCCCAACGAACTAGCTCCTCTCGGATGACTTAGAACGCCACTCCT
* *
38411 TCAAGCTTTTCACGGAGAAATGCCACGGTAAGTAAGACTGACGGAGAAAAGTAAGGCCTTCTCTC
196 TCAAGCTTGTCACGGAGAAATGCCACGGCAAGTAAGACTGACGGAGAAAAGTAAGGCCTTCTCTC
* * * * *
38476 TCTAACTTTTAAGCTCAAAATGGCATGGAACCAAAGTGTATAACATTGTGGCTTCATCCTTTATT
261 TCTAACTTTTAAGCTCAAAATGGAATCGAACCAAAGTGCATAACATTATGGCTTCATCCGTTATT
*
38541 TATAGGGGAGAAAAACCCTAAAGATTTGTGTCAAAATTCCAAAGATACCCAAATCATGTTTAATT
326 TATAGGGGAGAAAAACCCTAAAGATTTGTGTCAAAATTCCAAAGATACCCAAATCATGCTTAATT
38606 CATGTGAGGATCGGGCAGACCTGGCAGTGGTGCTACTGGGCAGCTGGCAATGGTCCAGCCTGGAT
391 CATGTGAGGATCGGGCAGACCTGGCAGTGGTGCTACTGGGCAGCTGGCAATGGTCCAGCCTGGAT
* ** * *
38671 GGTTGACTGAGCACCCGACAGACAGTACTGATTCAGGCGGATTTCTCAGTCATGCTCAGATATCT
456 GGTAGACTGAGCACCCGACAGACAACACTGATTCAGGCGGATTTCTCAGTCATGCTCAGAGATCC
*
38736 CGTGAAAATAGGGACAGCTGGCTCCAAAAATATCTTCTTTCATTTTGTTTGCTCTCGAAATACCA
521 CGTGAAAATAGGGACAGCTGGCTCCAAAAATATCTTCTTTCATTTTGTTCGCTCTCGAAATACCA
* *
38801 ATCC-ACTCGGCATTTTCATTCTACTCAGCAATCTCCTTATGCCACGACATTTTCCTTTTTCTTT
586 ATCCAACTCGGCATTTTCATTCTACTCAGCAATCTCCTTATGCAACAACATTTTCCTTTTTCTTT
* *
38865 TCCTTACTCTCAAATCCTACATATCATTAAGCAAACACCTTCCCCATAAGGCAGCACTGATGACA
651 TCCTTACTCTCAAATCCTACACATCATTAAGCAAACACCTTCCCCATAAGGCACCACTGATGACA
* * * *
38930 AATTAAAATATCGTGGCAAACCTAATTCCATCACATGCAACTATATGCTCCTAAATGCATCTATG
716 AATTAAAATATCGCGACAAACCTAATTCCACCACATGCAACTATATACTCCTAAATGCATCTATG
38995 TGGTCCTAAATGAGCTCTTAGACA
781 TGGTCCTAAATGAGCTCTTAGACA
* *
39019 TTCATGGTGGGGTTCGAAATAAACAAGCACAAGTCAAGTTTCATTCGTTTCTTACAACCCAATAA
1 TTCATGGTGGGGTTCGAAATAAACAAGCACAAGTCAAGTTTAATTCGTTCCTTACAACCCAATAA
*
39084 CAAAATATGAAAGTAAAAAACTAAGGGAATGAGGAAAAGCCTTCGACGTGCACTGCTAGAGCTTC
66 CAAAATATGAAAGCAAAAAACTAAGGGAATGAGGAAAAGCCTTCGACGTGCACTGCTAGAGCTTC
* *
39149 CCTTGGTCACCACGAACTGCCCCCAGCGAACTAGCTCCTCTCGGATGACTTAGAACGCCACTCCT
131 CCTTGGTCACCACAAACTGCCCCCAACGAACTAGCTCCTCTCGGATGACTTAGAACGCCACTCCT
39214 TCAAGCTTGTCACGGAGAAATGCCACGGCAAGTAAGACTGACGGAGAAAAGTAAGGCCTTCTCTC
196 TCAAGCTTGTCACGGAGAAATGCCACGGCAAGTAAGACTGACGGAGAAAAGTAAGGCCTTCTCTC
39279 TCTAACTTTTAAGCTCAAAATGGAATCGAACCAAAGTGCATAACATTATGGCTTCATCCGTTATT
261 TCTAACTTTTAAGCTCAAAATGGAATCGAACCAAAGTGCATAACATTATGGCTTCATCCGTTATT
* * *
39344 TATAGGGGAGAAAACCCCTAAAGATTTGTGTTAAAATTCTAAAGATACCCAAATCATGCTTAATT
326 TATAGGGGAGAAAAACCCTAAAGATTTGTGTCAAAATTCCAAAGATACCCAAATCATGCTTAATT
* * ** * *
39409 CATGTGTGGATCGGGCAGAGCTGGCAGTGGTGCTGTTGGGTAGCTGGCAATGGTCCAGCTTGGAT
391 CATGTGAGGATCGGGCAGACCTGGCAGTGGTGCTACTGGGCAGCTGGCAATGGTCCAGCCTGGAT
* * * * *
39474 GGTAGACTGAGTACCCTACAGACAACATTGATTCAGGCGGATTTCTCAGTCATGGTCTGAGATCC
456 GGTAGACTGAGCACCCGACAGACAACACTGATTCAGGCGGATTTCTCAGTCATGCTCAGAGATCC
* **
39539 CGTGAAAATAGGGACAGCTGGCTCCACAAATATCTTCTTTCATTTTGTTCGCTCTCGAAATGTCA
521 CGTGAAAATAGGGACAGCTGGCTCCAAAAATATCTTCTTTCATTTTGTTCGCTCTCGAAATACCA
* ** *
39604 ATCCAACTCGGCATTTTCATTTTGTTCAGCAATCTCCTTATGCAACAACATTTTTCTTTTTCTTT
586 ATCCAACTCGGCATTTTCATTCTACTCAGCAATCTCCTTATGCAACAACATTTTCCTTTTTCTTT
* ** * *
39669 TCCTTGCTCTCAAATTTTGCACATCATTAATCAAACACCTTCCCCATAAGGCACCACTGATGACA
651 TCCTTACTCTCAAATCCTACACATCATTAAGCAAACACCTTCCCCATAAGGCACCACTGATGACA
* *
39734 AATTAAAATGTCGCGACAAACCTAATTCCACCACATGCAACTATATACTCCTAAATGCTTCTATG
716 AATTAAAATATCGCGACAAACCTAATTCCACCACATGCAACTATATACTCCTAAATGCATCTATG
*
39799 TGGTCCTAAATGATCTCTTAGACA
781 TGGTCCTAAATGAGCTCTTAGACA
39823 TTCA
1 TTCA
39827 ATAACTTAAG
Statistics
Matches: 749, Mismatches: 58, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
803 551 0.74
804 198 0.26
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (804 bp):
TTCATGGTGGGGTTCGAAATAAACAAGCACAAGTCAAGTTTAATTCGTTCCTTACAACCCAATAA
CAAAATATGAAAGCAAAAAACTAAGGGAATGAGGAAAAGCCTTCGACGTGCACTGCTAGAGCTTC
CCTTGGTCACCACAAACTGCCCCCAACGAACTAGCTCCTCTCGGATGACTTAGAACGCCACTCCT
TCAAGCTTGTCACGGAGAAATGCCACGGCAAGTAAGACTGACGGAGAAAAGTAAGGCCTTCTCTC
TCTAACTTTTAAGCTCAAAATGGAATCGAACCAAAGTGCATAACATTATGGCTTCATCCGTTATT
TATAGGGGAGAAAAACCCTAAAGATTTGTGTCAAAATTCCAAAGATACCCAAATCATGCTTAATT
CATGTGAGGATCGGGCAGACCTGGCAGTGGTGCTACTGGGCAGCTGGCAATGGTCCAGCCTGGAT
GGTAGACTGAGCACCCGACAGACAACACTGATTCAGGCGGATTTCTCAGTCATGCTCAGAGATCC
CGTGAAAATAGGGACAGCTGGCTCCAAAAATATCTTCTTTCATTTTGTTCGCTCTCGAAATACCA
ATCCAACTCGGCATTTTCATTCTACTCAGCAATCTCCTTATGCAACAACATTTTCCTTTTTCTTT
TCCTTACTCTCAAATCCTACACATCATTAAGCAAACACCTTCCCCATAAGGCACCACTGATGACA
AATTAAAATATCGCGACAAACCTAATTCCACCACATGCAACTATATACTCCTAAATGCATCTATG
TGGTCCTAAATGAGCTCTTAGACA
Found at i:41229 original size:64 final size:65
Alignment explanation
Indices: 41153--41276 Score: 189
Period size: 64 Copynumber: 1.9 Consensus size: 65
41143 AAAATCTTAT
*
41153 ATCCTAATTAAAACACTTAAAA-CAATCTAAACTAAAATACCTAAAA-AAATATATAATATTATA
1 ATCCTAATTAAAACAC-TAAAACCAATCTAAACTAAAATACCTAAAACAAATATAAAATATTATA
41216 A
65 A
* * *
41217 ATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATAT
1 ATCCTAATTAAAACACTAAAACCAATCTAAACTAAAATACCTAAAACAAATATAAAATAT
41277 AAAAATAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
63 5 0.09
64 37 0.69
65 12 0.22
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (65 bp):
ATCCTAATTAAAACACTAAAACCAATCTAAACTAAAATACCTAAAACAAATATAAAATATTATAA
Found at i:41241 original size:19 final size:19
Alignment explanation
Indices: 41214--41323 Score: 59
Period size: 19 Copynumber: 5.8 Consensus size: 19
41204 TATAATATTA
*
41214 TAAATCCTAATTAAAATAC
1 TAAAACCTAATTAAAATAC
* *
41233 TAAAACCTATTTAAACTA-
1 TAAAACCTAATTAAAATAC
*
41251 -AAATACCTAA-AACAAATA-
1 TAAA-ACCTAATTA-AAATAC
** *
41269 TAAAATATAA-AAATAATATCC
1 TAAAACCTAATTAA-AATA--C
*
41290 TAAAACTTAATTAAAATAC
1 TAAAACCTAATTAAAATAC
*
41309 TAAAACCTATTTAAA
1 TAAAACCTAATTAAA
41324 CTAAAATACA
Statistics
Matches: 70, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
17 5 0.07
18 19 0.27
19 32 0.46
21 12 0.17
22 2 0.03
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAACCTAATTAAAATAC
Found at i:41272 original size:25 final size:24
Alignment explanation
Indices: 41225--41272 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
41215 AAATCCTAAT
** *
41225 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAATATAAAC
41249 TAAAATACCTAAAACAAATATAAA
1 TAAAATA-CTAAAACAAATATAAA
41273 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAAATATAAAC
Found at i:41293 original size:32 final size:32
Alignment explanation
Indices: 41252--41313 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
41242 TTTAAACTAA
41252 AATACCTAAAAC-AAATATAAAATA-TAAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAAT
*
41283 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAA
41314 CCTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (32 bp):
AATACCTAAAACTAAATTAAAATACTAAAAAT
Found at i:41356 original size:76 final size:75
Alignment explanation
Indices: 41221--41368 Score: 210
Period size: 76 Copynumber: 2.0 Consensus size: 75
41211 TTATAAATCC
*
41221 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATAAAAATAAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAAAATATAAAATAT-AAAATAAT
41286 ATCCTAAAACT
65 ATCCTAAAACT
** * *
41297 TAATTAAAATACTAAAACCTATTTAAACTAAAATA-C-AAATATAAAATATAATGTTTAAAATAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAA-A-AAAATATAAAATATAAAATAA
41360 TATCCTAAA
64 TATCCTAAA
41369 CTTGAGTTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
74 3 0.05
75 17 0.26
76 45 0.69
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.30
Consensus pattern (75 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAAAATATAAAATATAAAATAATA
TCCTAAAACT
Found at i:45955 original size:4 final size:4
Alignment explanation
Indices: 45948--45973 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
45938 ATAAAATAAA
45948 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
45974 AAAGATCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:46639 original size:64 final size:63
Alignment explanation
Indices: 46563--46681 Score: 186
Period size: 64 Copynumber: 1.9 Consensus size: 63
46553 AACATCTTAG
46563 ATCCTAATTAAAACACTTAAAA-CTATCTAAACTAAAATACCTAAAAAATAATATAATATTTTAA
1 ATCCTAATTAAAACAC-TAAAACCTATCTAAACTAAAATACCTAAAAAA-AATATAATATTTTAA
* * *
46627 ATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAATATAA
1 ATCCTAATTAAAACACTAAAACCTATCTAAACTAAAATACCTAAAAAAAATATAA
46682 AATATAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
63 12 0.24
64 39 0.76
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.30
Consensus pattern (63 bp):
ATCCTAATTAAAACACTAAAACCTATCTAAACTAAAATACCTAAAAAAAATATAATATTTTAA
Found at i:46766 original size:76 final size:75
Alignment explanation
Indices: 46604--46778 Score: 192
Period size: 76 Copynumber: 2.3 Consensus size: 75
46594 CTAAAATACC
* * ** * * * *
46604 TAAAAAATAATATAATATTTTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT
1 TAAAATATAAAATAATATCCTAAAACTTAATTAAAACACTAAAACCTATTTAAAATAAAATACCT
46669 AAAATAAATA
66 AAAATAAATA
*
46679 TAAAATATAAAAATAATATCCTAAAACTTAATTAAAACACTAATACCTATTTAAAATAAAATA-C
1 TAAAATAT-AAAATAATATCCTAAAACTTAATTAAAACACTAAAACCTATTTAAAATAAAATACC
46743 -AAAGATAAAATA
65 TAAA-AT-AAATA
** * *
46755 TAATGTTTAAAATATTATCCTAAA
1 TAAAATATAAAATAATATCCTAAA
46779 CTTGAGTTTA
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
74 3 0.04
75 25 0.30
76 56 0.67
ACGTcount: A:0.57, C:0.10, G:0.01, T:0.31
Consensus pattern (75 bp):
TAAAATATAAAATAATATCCTAAAACTTAATTAAAACACTAAAACCTATTTAAAATAAAATACCT
AAAATAAATA
Found at i:52744 original size:15 final size:15
Alignment explanation
Indices: 52726--52754 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52716 GAAAAGAAGA
52726 AAAGTGAAGAGAAAC
1 AAAGTGAAGAGAAAC
52741 AAAGTGAAGAGAAA
1 AAAGTGAAGAGAAA
52755 GAAGATGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.03, G:0.28, T:0.07
Consensus pattern (15 bp):
AAAGTGAAGAGAAAC
Found at i:54637 original size:35 final size:36
Alignment explanation
Indices: 54537--54641 Score: 140
Period size: 36 Copynumber: 2.9 Consensus size: 36
54527 TAATAAGAAG
* * *
54537 AACGAAAGGAAACATCGACACTTTCGATTCAAGTCG
1 AACGGAAGGAAGCATCGACACTTTCGATTCAAGTCA
54573 AACGGAAGGAAGCATCGACACTTTCGATTCAAGTCA
1 AACGGAAGGAAGCATCGACACTTTCGATTCAAGTCA
* ** *
54609 AACGGAAGGAGGTGTC-TCACTTTCGATTCAAGT
1 AACGGAAGGAAGCATCGACACTTTCGATTCAAGT
54642 GTTCATCTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 16 0.26
36 46 0.74
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (36 bp):
AACGGAAGGAAGCATCGACACTTTCGATTCAAGTCA
Found at i:55306 original size:23 final size:23
Alignment explanation
Indices: 55288--55348 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
55278 CTCGTATAAA
55288 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
55311 TACACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
55334 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
55349 TATAAGATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:56062 original size:63 final size:64
Alignment explanation
Indices: 55994--56149 Score: 165
Period size: 63 Copynumber: 2.5 Consensus size: 64
55984 TAACGGGTGT
* * * * *
55994 ATCGATGCACTA-TCTATGCATCGGTGCA-TAAATCCCATTCGATGTTTGTA-TTTAATGGAGTG
1 ATCGATGCACTACT-TATGCATCGATACACT-AATCACATTCGATGTTTGTATTTTAAAGAAGTG
56056 C
64 C
* * *
56057 ATCGATGCACTACTTGTGCATCGATACACTAATGACATTCGATGTTTTTATTTTAAAGAAGTGC
1 ATCGATGCACTACTTATGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAAGAAGTGC
* * * *
56121 ATCGATGCACTTCATGTGCATCAATACAC
1 ATCGATGCACTACTTATGCATCGATACAC
56150 CTTGAACGAT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
63 40 0.51
64 39 0.49
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (64 bp):
ATCGATGCACTACTTATGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAAGAAGTGC
Found at i:56139 original size:64 final size:63
Alignment explanation
Indices: 56029--56149 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 63
56019 GCATAAATCC
* * * *
56029 CATTCGATGTTTGTATTTAATGGAGTGCATCGATGCACTACTTGTGCATCGATACACTAATGA
1 CATTCGATGTTTGTATTTAAAGAAGTGCATCGATGCACTACATGTGCATCAATACACTAATGA
* *
56092 CATTCGATGTTTTTATTTTAAAGAAGTGCATCGATGCACTTCATGTGCATCAATACAC
1 CATTCGATGTTTGTA-TTTAAAGAAGTGCATCGATGCACTACATGTGCATCAATACAC
56150 CTTGAACGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
63 14 0.27
64 37 0.73
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (63 bp):
CATTCGATGTTTGTATTTAAAGAAGTGCATCGATGCACTACATGTGCATCAATACACTAATGA
Done.